Loc device for amplifying and detecting target nucleic acid sequences using electrochemiluminescent resonant energy transfer, stem-and-loop probes with covalently attached primers

ABSTRACT

A lab-on-a-chip (LOC) device for amplifying and detecting target nucleic acid sequences, the LOC device having electrochemiluminescent (ECL), resonant energy transfer, stem-and-loop probes for hybridization with the target nucleic acid sequences, each of the probes having a loop portion containing a sequence complementary to the target nucleic acid sequence, an ECL luminophore for emitting photons when in an excited state, a functional moiety for quenching photon emission from the ECL luminophore by resonant energy transfer, and a covalently attached primer for extension along a complementary sequence denatured from the target nucleic acid sequence to replicate the target nucleic acid sequence, heaters for thermally cycling the target nucleic acid sequences through a polymerase chain reaction (PCR), in which the covalently attached primers anneal to oligonucleotides containing the target nucleic acid sequences, and, electrodes for receiving an electrical pulse to excite the ECL luminophores, wherein during use, replicating the target nucleic acid sequence causes the loop portion to open such the complementary nucleic acid sequence therein hybridizes to the target nucleic acid sequence and the ECL luminophore is moved away from the functional moiety.

FIELD OF THE INVENTION

The present invention relates to diagnostic devices that usemicrosystems technologies (MST). In particular, the invention relates tomicrofluidic and biochemical processing and analysis for moleculardiagnostics.

CO-PENDING APPLICATIONS

The following applications have been filed by the Applicant which relateto the present application:

GBS001US GBS002US GBS003US GBS005US GBS006US GSR001US GSR002US GAS001USGAS002US GAS003US GAS004US GAS006US GAS007US GAS008US GAS009US GAS010USGAS012US GAS013US GAS014US GAS015US GAS016US GAS017US GAS018US GAS019USGAS020US GAS021US GAS022US GAS023US GAS024US GAS025US GAS026US GAS027USGAS028US GAS030US GAS031US GAS032US GAS033US GAS034US GAS035US GAS036USGAS037US GAS038US GAS039US GAS040US GAS041US GAS042US GAS043US GAS044USGAS045US GAS046US GAS047US GAS048US GAS049US GAS050US GAS054US GAS055USGAS056US GAS057US GAS058US GAS059US GAS060US GAS061US GAS062US GAS063USGAS065US GAS066US GAS067US GAS068US GAS069US GAS070US GAS080US GAS081USGAS082US GAS083US GAS084US GAS085US GAS086US GAS087US GAS088US GAS089USGAS090US GAS091US GAS092US GAS093US GAS094US GAS095US GAS096US GAS097USGAS098US GAS099US GAS100US GAS101US GAS102US GAS103US GAS104US GAS105USGAS106US GAS108US GAS109US GAS110US GAS111US GAS112US GAS113US GAS114USGAS115US GAS118US GAS119US GAS120US GAS121US GAS122US GAS123US GAS124USGAS125US GAS126US GAS127US GAS128US GAS129US GAS130US GAS131US GAS132USGAS133US GAS134US GAS135US GAS136US GAS137US GAS138US GAS139US GAS140USGAS141US GAS142US GAS143US GAS144US GAS146US GAS147US GRR001US GRR002USGRR003US GRR004US GRR005US GRR006US GRR007US GRR008US GRR009US GRR010USGVA001US GVA002US GVA004US GVA005US GVA006US GVA007US GVA008US GVA009USGVA010US GVA011US GVA012US GVA013US GVA014US GVA015US GVA016US GVA017USGVA018US GVA019US GVA020US GVA021US GVA022US GHU001US GHU002US GHU003USGHU004US GHU006US GHU007US GHU008US GWM001US GWM002US GDI001US GDI002USGDI003US GDI004US GDI005US GDI006US GDI007US GDI009US GDI010US GDI011USGDI013US GDI014US GDI015US GDI016US GDI017US GDI019US GDI023US GDI028USGDI030US GDI039US GDI040US GDI041US GPC001US GPC002US GPC003US GPC004USGPC005US GPC006US GPC007US GPC008US GPC009US GPC010US GPC011US GPC012USGPC014US GPC017US GPC018US GPC019US GPC023US GPC027US GPC028US GPC029USGPC030US GPC031US GPC033US GPC034US GPC035US GPC036US GPC037US GPC038USGPC039US GPC040US GPC041US GPC042US GPC043US GLY001US GLY002US GLY003USGLY004US GLY005US GLY006US GIN001US GIN002US GIN003US GIN004US GIN005USGIN006US GIN007US GIN008US GMI001US GMI002US GMI005US GMI008US GLE001USGLE002US GLE003US GLE004US GLE005US GLE006US GLE007US GLE008US GLE009USGLE010US GLE011US GLE012US GLE013US GLE014US GLA001US GGA001US GGA003USGRE001US GRE002US GRE003US GRE004US GRE005US GRE006US GRE007US GCF001USGCF002US GCF003US GCF004US GCF005US GCF006US GCF007US GCF008US GCF009USGCF010US GCF011US GCF012US GCF013US GCF014US GCF015US GCF016US GCF020USGCF021US GCF022US GCF023US GCF024US GCF025US GCF027US GCF028US GCF029USGCF030US GCF031US GCF032US GCF033US GCF034US GCF035US GCF036US GCF037USGSA001US GSA002US GSE001US GSE002US GSE003US GSE004US GDA001US GDA002USGDA003US GDA004US GDA005US GDA006US GDA007US GPK001US GMO001US GMV001USGMV002US GMV003US GMV004US GRD001US GRD002US GRD003US GRD004US GPD001USGPD003US GPD004US GPD005US GPD006US GPD007US GPD008US GPD009US GPD010USGPD011US GPD012US GPD013US GPD014US GPD015US GPD016US GPD017US GAL001USGPA001US GPA003US GPA004US GPA005US GSS001US GSL001US GCA001US GCA002USGCA003US

The disclosures of these co-pending applications are incorporated hereinby reference. The above applications have been identified by theirfiling docket number, which will be substituted with the correspondingapplication number, once assigned.

BACKGROUND OF THE INVENTION

Molecular diagnostics has emerged as a field that offers the promise ofearly disease detection, potentially before symptoms have manifested.Molecular diagnostic testing is used to detect:

-   -   Inherited disorders    -   Acquired disorders    -   Infectious diseases    -   Genetic predisposition to health-related conditions.

With high accuracy and fast turnaround times, molecular diagnostic testshave the potential to reduce the occurrence of ineffective health careservices, enhance patient outcomes, improve disease management andindividualize patient care. Many of the techniques in moleculardiagnostics are based on the detection and identification of specificnucleic acids, both deoxyribonucleic acid (DNA) and ribonucleic acid(RNA), extracted and amplified from a biological specimen (such as bloodor saliva). The complementary nature of the nucleic acid bases allowsshort sequences of synthesized DNA (oligonucleotides) to bond(hybridize) to specific nucleic acid sequences for use in nucleic acidtests. If hybridization occurs, then the complementary sequence ispresent in the sample. This makes it possible, for example, to predictthe disease a person will contract in the future, determine the identityand virulence of an infectious pathogen, or determine the response aperson will have to a drug.

Nucleic Acid Based Molecular Diagnostic Test

A nucleic acid based test has four distinct steps:

1. Sample preparation

2. Nucleic acid extraction

3. Nucleic acid amplification (optional)

4. Detection

Many sample types are used for genetic analysis, such as blood, urine,sputum and tissue samples. The diagnostic test determines the type ofsample required as not all samples are representative of the diseaseprocess. These samples have a variety of constituents, but usually onlyone of these is of interest. For example, in blood, high concentrationsof erythrocytes can inhibit the detection of a pathogenic organism.Therefore a purification and/or concentration step at the beginning ofthe nucleic acid test is often required.

Blood is one of the more commonly sought sample types. It has threemajor constituents: leukocytes (white blood cells), erythrocytes (redblood cells) and thrombocytes (platelets). The thrombocytes facilitateclotting and remain active in vitro. To inhibit coagulation, thespecimen is mixed with an agent such as ethylenediaminetetraacetic acid(EDTA) prior to purification and concentration. Erythrocytes are usuallyremoved from the sample in order to concentrate the target cells. Inhumans, erythrocytes account for approximately 99% of the cellularmaterial but do not carry DNA as they have no nucleus. Furthermore,erythrocytes contain components such as haemoglobin that can interferewith the downstream nucleic acid amplification process (describedbelow). Removal of erythrocytes can be achieved by differentially lysingthe erythrocytes in a lysis solution, leaving remaining cellularmaterial intact which can then be separated from the sample usingcentrifugation. This provides a concentration of the target cells fromwhich the nucleic acids are extracted.

The exact protocol used to extract nucleic acids depends on the sampleand the diagnostic assay to be performed. For example, the protocol forextracting viral RNA will vary considerably from the protocol to extractgenomic DNA. However, extracting nucleic acids from target cells usuallyinvolves a cell lysis step followed by nucleic acid purification. Thecell lysis step disrupts the cell and nuclear membranes, releasing thegenetic material. This is often accomplished using a lysis detergent,such as sodium dodecyl sulfate, which also denatures the large amount ofproteins present in the cells.

The nucleic acids are then purified with an alcohol precipitation step,usually ice-cold ethanol or isopropanol, or via a solid phasepurification step, typically on a silica matrix in a column, resin or onparamagnetic beads in the presence of high concentrations of achaotropic salt, prior to washing and then elution in a low ionicstrength buffer. An optional step prior to nucleic acid precipitation isthe addition of a protease which digests the proteins in order tofurther purify the sample.

Other lysis methods include mechanical lysis via ultrasonic vibrationand thermal lysis where the sample is heated to 94° C. to disrupt cellmembranes.

The target DNA or RNA may be present in the extracted material in verysmall amounts, particularly if the target is of pathogenic origin.Nucleic acid amplification provides the ability to selectively amplify(that is, replicate) specific targets present in low concentrations todetectable levels.

The most commonly used nucleic acid amplification technique is thepolymerase chain reaction (PCR). PCR is well known in this field andcomprehensive description of this type of reaction is provided in E. vanPelt-Verkuil et al., Principles and Technical Aspects of PCRAmplification, Springer, 2008.

PCR is a powerful technique that amplifies a target DNA sequence againsta background of complex DNA. If RNA is to be amplified (by PCR), it mustbe first transcribed into cDNA (complementary DNA) using an enzymecalled reverse transcriptase. Afterwards, the resulting cDNA isamplified by PCR.

PCR is an exponential process that proceeds as long as the conditionsfor sustaining the reaction are acceptable. The components of thereaction are:

1. pair of primers—short single strands of DNA with around 10-30nucleotides complementary to the regions flanking the target sequence

2. DNA polymerase—a thermostable enzyme that synthesizes DNA

3. deoxyribonucleoside triphosphates (dNTPs)—provide the nucleotidesthat are incorporated into the newly synthesized DNA strand

4. buffer—to provide the optimal chemical environment for DNA synthesis

PCR typically involves placing these reactants in a small tube (˜10-50microlitres) containing the extracted nucleic acids. The tube is placedin a thermal cycler; an instrument that subjects the reaction to aseries of different temperatures for varying amounts of time. Thestandard protocol for each thermal cycle involves a denaturation phase,an annealing phase, and an extension phase. The extension phase issometimes referred to as the primer extension phase. In addition to suchthree-step protocols, two-step thermal protocols can be employed, inwhich the annealing and extension phases are combined. The denaturationphase typically involves raising the temperature of the reaction to90-95° C. to denature the DNA strands; in the annealing phase, thetemperature is lowered to ˜50-60° C. for the primers to anneal; and thenin the extension phase the temperature is raised to the optimal DNApolymerase activity temperature of 60-72° C. for primer extension. Thisprocess is repeated cyclically around 20-40 times, the end result beingthe creation of millions of copies of the target sequence between theprimers.

There are a number of variants to the standard PCR protocol such asmultiplex PCR, linker-primed PCR, direct PCR, tandem PCR, real-time PCRand reverse-transcriptase PCR, amongst others, which have been developedfor molecular diagnostics.

Multiplex PCR uses multiple primer sets within a single PCR mixture toproduce amplicons of varying sizes that are specific to different DNAsequences. By targeting multiple genes at once, additional informationmay be gained from a single test-run that otherwise would requireseveral experiments. Optimization of multiplex PCR is more difficultthough and requires selecting primers with similar annealingtemperatures, and amplicons with similar lengths and base composition toensure the amplification efficiency of each amplicon is equivalent.

Linker-primed PCR, also known as ligation adaptor PCR, is a method usedto enable nucleic acid amplification of essentially all DNA sequences ina complex DNA mixture without the need for target-specific primers. Themethod firstly involves digesting the target DNA population with asuitable restriction endonuclease (enzyme). Double-strandedoligonucleotide linkers (also called adaptors) with a suitableoverhanging end are then ligated to the ends of target DNA fragmentsusing a ligase enzyme. Nucleic acid amplification is subsequentlyperformed using oligonucleotide primers which are specific for thelinker sequences. In this way, all fragments of the DNA source which areflanked by linker oligonucleotides can be amplified.

Direct PCR describes a system whereby PCR is performed directly on asample without any, or with minimal, nucleic acid extraction. It haslong been accepted that PCR reactions are inhibited by the presence ofmany components of unpurified biological samples, such as the haemcomponent in blood. Traditionally, PCR has required extensivepurification of the target nucleic acid prior to preparation of thereaction mixture. With appropriate changes to the chemistry and sampleconcentration, however, it is possible to perform PCR with minimal DNApurification, or direct PCR. Adjustments to the PCR chemistry for directPCR include increased buffer strength, the use of polymerases which havehigh activity and processivity, and additives which chelate withpotential polymerase inhibitors.

Tandem PCR utilises two distinct rounds of nucleic acid amplification toincrease the probability that the correct amplicon is amplified. Oneform of tandem PCR is nested PCR in which two pairs of PCR primers areused to amplify a single locus in separate rounds of nucleic acidamplification. The first pair of primers hybridize to the nucleic acidsequence at regions external to the target nucleic acid sequence. Thesecond pair of primers (nested primers) used in the second round ofamplification bind within the first PCR product and produce a second PCRproduct containing the target nucleic acid, that will be shorter thanthe first one. The logic behind this strategy is that if the wrong locuswere amplified by mistake during the first round of nucleic acidamplification, the probability is very low that it would also beamplified a second time by a second pair of primers and thus ensuresspecificity.

Real-time PCR, or quantitative PCR, is used to measure the quantity of aPCR product in real time. By using a fluorophore-containing probe orfluorescent dyes along with a set of standards in the reaction, it ispossible to quantitate the starting amount of nucleic acid in thesample. This is particularly useful in molecular diagnostics wheretreatment options may differ depending on the pathogen load in thesample.

Reverse-transcriptase PCR (RT-PCR) is used to amplify DNA from RNA.Reverse transcriptase is an enzyme that reverse transcribes RNA intocomplementary DNA (cDNA), which is then amplified by PCR. RT-PCR iswidely used in expression profiling, to determine the expression of agene or to identify the sequence of an RNA transcript, includingtranscription start and termination sites. It is also used to amplifyRNA viruses such as human immunodeficiency virus or hepatitis C virus.

Isothermal amplification is another form of nucleic acid amplificationwhich does not rely on the thermal denaturation of the target DNA duringthe amplification reaction and hence does not require sophisticatedmachinery. Isothermal nucleic acid amplification methods can thereforebe carried out in primitive sites or operated easily outside of alaboratory environment. A number of isothermal nucleic acidamplification methods have been described, including Strand DisplacementAmplification, Transcription Mediated Amplification, Nucleic AcidSequence Based Amplification, Recombinase Polymerase Amplification,Rolling Circle Amplification, Ramification Amplification,Helicase-Dependent Isothermal DNA Amplification and Loop-MediatedIsothermal Amplification.

Isothermal nucleic acid amplification methods do not rely on thecontinuing heat denaturation of the template DNA to produce singlestranded molecules to serve as templates for further amplification, butinstead rely on alternative methods such as enzymatic nicking of DNAmolecules by specific restriction endonucleases, or the use of an enzymeto separate the DNA strands, at a constant temperature.

Strand Displacement Amplification (SDA) relies on the ability of certainrestriction enzymes to nick the unmodified strand of hemi-modified DNAand the ability of a 5′-3′ exonuclease-deficient polymerase to extendand displace the downstream strand. Exponential nucleic acidamplification is then achieved by coupling sense and antisense reactionsin which strand displacement from the sense reaction serves as atemplate for the antisense reaction. The use of nickase enzymes which donot cut DNA in the traditional manner but produce a nick on one of theDNA strands, such as N. Alw1, N. BstNB1 and Mly1, are useful in thisreaction. SDA has been improved by the use of a combination of aheat-stable restriction enzyme (Ava1) and heat-stable Exo-polymerase(Bst polymerase). This combination has been shown to increaseamplification efficiency of the reaction from 10⁸ fold amplification to10¹⁰ fold amplification so that it is possible using this technique toamplify unique single copy molecules.

Transcription Mediated Amplification (TMA) and Nucleic Acid SequenceBased Amplification (NASBA) use an RNA polymerase to copy RNA sequencesbut not corresponding genomic DNA. The technology uses two primers andtwo or three enzymes, RNA polymerase, reverse transcriptase andoptionally RNase H (if the reverse transcriptase does not have RNaseactivity). One primer contains a promoter sequence for RNA polymerase.In the first step of nucleic acid amplification, this primer hybridizesto the target ribosomal RNA (rRNA) at a defined site. Reversetranscriptase creates a DNA copy of the target rRNA by extension fromthe 3′ end of the promoter primer. The RNA in the resulting RNA:DNAduplex is degraded by the RNase activity of the reverse transcriptase ifpresent or the additional RNase H. Next, a second primer binds to theDNA copy. A new strand of DNA is synthesized from the end of this primerby reverse transcriptase, creating a double-stranded DNA molecule. RNApolymerase recognizes the promoter sequence in the DNA template andinitiates transcription. Each of the newly synthesized RNA ampliconsre-enters the process and serves as a template for a new round ofreplication.

In Recombinase Polymerase Amplification (RPA), the isothermalamplification of specific DNA fragments is achieved by the binding ofopposing oligonucleotide primers to template DNA and their extension bya DNA polymerase. Heat is not required to denature the double-strandedDNA (dsDNA) template. Instead, RPA employs recombinase-primer complexesto scan dsDNA and facilitate strand exchange at cognate sites. Theresulting structures are stabilised by single-stranded DNA bindingproteins interacting with the displaced template strand, thus preventingthe ejection of the primer by branch migration. Recombinase disassemblyleaves the 3′ end of the oligonucleotide accessible to a stranddisplacing DNA polymerase, such as the large fragment of Bacillussubtilis Pol I (Bsu), and primer extension ensues. Exponential nucleicacid amplification is accomplished by the cyclic repetition of thisprocess.

Helicase-dependent amplification (HDA) mimics the in vivo system in thatit uses a DNA helicase enzyme to generate single-stranded templates forprimer hybridization and subsequent primer extension by a DNApolymerase. In the first step of the HDA reaction, the helicase enzymetraverses along the target DNA, disrupting the hydrogen bonds linkingthe two strands which are then bound by single-stranded bindingproteins. Exposure of the single-stranded target region by the helicaseallows primers to anneal. The DNA polymerase then extends the 3′ ends ofeach primer using free deoxyribonucleoside triphosphates (dNTPs) toproduce two DNA replicates. The two replicated dsDNA strandsindependently enter the next cycle of HDA, resulting in exponentialnucleic acid amplification of the target sequence.

Other DNA-based isothermal techniques include Rolling CircleAmplification (RCA) in which a DNA polymerase extends a primercontinuously around a circular DNA template, generating a long DNAproduct that consists of many repeated copies of the circle. By the endof the reaction, the polymerase generates many thousands of copies ofthe circular template, with the chain of copies tethered to the originaltarget DNA. This allows for spatial resolution of target and rapidnucleic acid amplification of the signal. Up to 10¹² copies of templatecan be generated in 1 hour. Ramification amplification is a variation ofRCA and utilizes a closed circular probe (C-probe) or padlock probe anda DNA polymerase with a high processivity to exponentially amplify theC-probe under isothermal conditions.

Loop-mediated isothermal amplification (LAMP), offers high selectivityand employs a DNA polymerase and a set of four specially designedprimers that recognize a total of six distinct sequences on the targetDNA. An inner primer containing sequences of the sense and antisensestrands of the target DNA initiates LAMP. The following stranddisplacement DNA synthesis primed by an outer primer releases asingle-stranded DNA. This serves as template for DNA synthesis primed bythe second inner and outer primers that hybridize to the other end ofthe target, which produces a stem-loop DNA structure. In subsequent LAMPcycling one inner primer hybridizes to the loop on the product andinitiates displacement DNA synthesis, yielding the original stem-loopDNA and a new stem-loop DNA with a stem twice as long. The cyclingreaction continues with accumulation of 10⁹ copies of target in lessthan an hour. The final products are stem-loop DNAs with severalinverted repeats of the target and cauliflower-like structures withmultiple loops formed by annealing between alternately inverted repeatsof the target in the same strand.

After completion of the nucleic acid amplification, the amplifiedproduct must be analysed to determine whether the anticipated amplicon(the amplified quantity of target nucleic acids) was generated. Themethods of analyzing the product range from simply determining the sizeof the amplicon through gel electrophoresis, to identifying thenucleotide composition of the amplicon using DNA hybridization.

Gel electrophoresis is one of the simplest ways to check whether thenucleic acid amplification process generated the anticipated amplicon.Gel electrophoresis uses an electric field applied to a gel matrix toseparate DNA fragments. The negatively charged DNA fragments will movethrough the matrix at different rates, determined largely by their size.After the electrophoresis is complete, the fragments in the gel can bestained to make them visible. Ethidium bromide is a commonly used stainwhich fluoresces under UV light.

The size of the fragments is determined by comparison with a DNA sizemarker (a DNA ladder), which contains DNA fragments of known sizes, runon the gel alongside the amplicon. Because the oligonucleotide primersbind to specific sites flanking the target DNA, the size of theamplified product can be anticipated and detected as a band of knownsize on the gel. To be certain of the identity of the amplicon, or ifseveral amplicons have been generated, DNA probe hybridization to theamplicon is commonly employed.

DNA hybridization refers to the formation of double-stranded DNA bycomplementary base pairing. DNA hybridization for positiveidentification of a specific amplification product requires the use of aDNA probe around 20 nucleotides in length. If the probe has a sequencethat is complementary to the amplicon (target) DNA sequence,hybridization will occur under favourable conditions of temperature, pHand ionic concentration. If hybridization occurs, then the gene or DNAsequence of interest was present in the original sample.

Optical detection is the most common method to detect hybridization.Either the amplicons or the probes are labelled to emit light throughfluorescence or electrochemiluminescence. These processes differ in themeans of producing excited states of the light-producing moieties, butboth enable covalent labelling of nucleotide strands. Inelectrochemiluminescence (ECL), light is produced by luminophoremolecules or complexes upon stimulation with an electric current. Influorescence, it is illumination with excitation light which leads toemission.

Fluorescence is detected using an illumination source which providesexcitation light at a wavelength absorbed by the fluorescent molecule,and a detection unit. The detection unit comprises a photosensor (suchas a photomultiplier tube or charge-coupled device (CCD) array) todetect the emitted signal, and a mechanism (such as awavelength-selective filter) to prevent the excitation light from beingincluded in the photosensor output. The fluorescent molecules emitStokes-shifted light in response to the excitation light, and thisemitted light is collected by the detection unit. Stokes shift is thefrequency difference or wavelength difference between emitted light andabsorbed excitation light.

ECL emission is detected using a photosensor which is sensitive to theemission wavelength of the ECL species being employed. For example,transition metal-ligand complexes emit light at visible wavelengths, soconventional photodiodes and CCDs are employed as photosensors. Anadvantage of ECL is that, if ambient light is excluded, the ECL emissioncan be the only light present in the detection system, which improvessensitivity.

Microarrays allow for hundreds of thousands of DNA hybridizationexperiments to be performed simultaneously. Microarrays are powerfultools for molecular diagnostics with the potential to screen forthousands of genetic diseases or detect the presence of numerousinfectious pathogens in a single test. A microarray consists of manydifferent DNA probes immobilized as spots on a substrate. The target DNA(amplicon) is first labelled with a fluorescent or luminescent molecule(either during or after nucleic acid amplification) and then applied tothe array of probes. The microarray is incubated in a temperaturecontrolled, humid environment for a number of hours or days whilehybridization between the probe and amplicon takes place. Followingincubation, the microarray must be washed in a series of buffers toremove unbound strands. Once washed, the microarray surface is driedusing a stream of air (often nitrogen). The stringency of thehybridization and washes is critical. Insufficient stringency can resultin a high degree of nonspecific binding. Excessive stringency can leadto a failure of appropriate binding, which results in diminishedsensitivity. Hybridization is recognized by detecting light emissionfrom the labelled amplicons which have formed a hybrid withcomplementary probes.

Fluorescence from microarrays is detected using a microarray scannerwhich is generally a computer controlled inverted scanning fluorescenceconfocal microscope which typically uses a laser for excitation of thefluorescent dye and a photosensor (such as a photomultiplier tube orCCD) to detect the emitted signal. The fluorescent molecules emitStokes-shifted light (described above) which is collected by thedetection unit.

The emitted fluorescence must be collected, separated from theunabsorbed excitation wavelength, and transported to the detector. Inmicroarray scanners, a confocal arrangement is commonly used toeliminate out-of-focus information by means of a confocal pinholesituated at an image plane. This allows only the in-focus portion of thelight to be detected. Light from above and below the plane of focus ofthe object is prevented from entering the detector, thereby increasingthe signal to noise ratio. The detected fluorescent photons areconverted into electrical energy by the detector which is subsequentlyconverted to a digital signal. This digital signal translates to anumber representing the intensity of fluorescence from a given pixel.Each feature of the array is made up of one or more such pixels. Thefinal result of a scan is an image of the array surface. The exactsequence and position of every probe on the microarray is known, and sothe hybridized target sequences can be identified and analysedsimultaneously.

More information regarding fluorescent probes can be found at:http://www.premierbiosoft.com/tech_notes/FRET_probe.html andhttp://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/Technical-Notes-and-Product-Highlights/Fluorescence-Resonance-Energy-Transfer-FRET.html

Point-of-Care Molecular Diagnostics

Despite the advantages that molecular diagnostic tests offer, the growthof this type of testing in the clinical laboratory has been slower thanexpected and remains a minor part of the practice of laboratorymedicine. This is primarily due to the complexity and costs associatedwith nucleic acid testing compared with tests based on methods notinvolving nucleic acids. The widespread adaptation of moleculardiagnostics testing to the clinical setting is intimately tied to thedevelopment of instrumentation that significantly reduces the cost,provides a rapid and automated assay from start (specimen processing) tofinish (generating a result) and operates without major intervention bypersonnel.

A point-of-care technology serving the physician's office, the hospitalbedside or even consumer-based, at home, would offer many advantagesincluding:

-   -   rapid availability of results enabling immediate facilitation of        treatment and improved quality of care.    -   ability to obtain laboratory values from testing very small        samples.    -   reduced clinical workload.    -   reduced laboratory workload and improved office efficiency by        reducing administrative work.    -   improved cost per patient through reduced length of stay of        hospitalization, conclusion of outpatient consultation at the        first visit, and reduced handling, storing and shipping of        specimens.    -   facilitation of clinical management decisions such as infection        control and antibiotic use.

Lab-on-a-Chip (LOC) Based Molecular Diagnostics

Molecular diagnostic systems based on microfluidic technologies providethe means to automate and speed up molecular diagnostic assays. Thequicker detection times are primarily due to the extremely low volumesinvolved, automation, and the low-overhead inbuilt cascading of thediagnostic process steps within a microfluidic device. Volumes in thenanoliter and microliter scale also reduce reagent consumption and cost.Lab-on-a-chip (LOC) devices are a common form of microfluidic device.LOC devices have MST structures within a MST layer for fluid processingintegrated onto a single supporting substrate (usually silicon).Fabrication using the VLSI (very large scale integrated) lithographictechniques of the semiconductor industry keeps the unit cost of each LOCdevice very low. However, controlling fluid flow through the LOC device,adding reagents, controlling reaction conditions and so on necessitatebulky external plumbing and electronics. Connecting a LOC device tothese external devices effectively restricts the use of LOC devices formolecular diagnostics to the laboratory setting. The cost of theexternal equipment and complexity of its operation precludes LOC-basedmolecular diagnostics as a practical option for point-of-care settings.

In view of the above, there is a need for a molecular diagnostic systembased on a LOC device for use at point-of-care.

SUMMARY OF THE INVENTION

Accordingly, the present invention provides a lab-on-a-chip (LOC) devicefor amplifying and detecting target nucleic acid sequences, the LOCdevice comprising:

electrochemiluminescent (ECL), resonant energy transfer, stem-and-loopprobes for hybridization with the target nucleic acid sequences, each ofthe probes having a loop portion containing a sequence complementary tothe target nucleic acid sequence, an ECL luminophore for emittingphotons when in an excited state, a functional moiety for quenchingphoton emission from the ECL luminophore by resonant energy transfer,and a covalently attached primer for extension along a complementarysequence denatured from the target nucleic acid sequence to replicatethe target nucleic acid sequence;

heaters for thermally cycling the target nucleic acid sequences througha polymerase chain reaction (PCR), in which the covalently attachedprimers anneal to oligonucleotides containing the target nucleic acidsequences; and,

electrodes for receiving an electrical pulse to excite the ECLluminophores; wherein during use,

replicating the target nucleic acid sequence causes the loop portion toopen such the complementary nucleic acid sequence therein hybridizes tothe target nucleic acid sequence and the ECL luminophore is moved awayfrom the functional moiety.

Preferably, the LOC device also has :

a photosensor for detecting light emitted by the ECL luminophores.

Preferably, the LOC device also has :

a supporting substrate;

CMOS circuitry for activating the heaters and providing the electrodeswith an electrical pulse;

hybridization chambers containing the probes for hybridization with thetargets, at least one of the heaters and a pair of the electrodes; and,

a flow-path for fluid containing the targets; wherein,

the CMOS circuitry is between the hybridization chambers and thesupporting substrate, and the flow-path draws the fluid to each of thehybridization chambers by capillary action.

Preferably, the LOC device also has a lysis section wherein the fluid isa biological sample containing cells and the lysis section disrupts thecellular membranes to release any genetic material therein.

Preferably, the hybridization chambers each have a wall section that isoptically transparent to the light emitted by the probes.

Preferably, the CMOS circuitry incorporates the photosensor wherein thewall section is positioned between the probes and the photosensor.

Preferably, the wall section is a layer incorporating silicon dioxide.

Preferably, the covalently attached primer is attached to the functionalmoiety for quenching photon emission from the ECL luminophore and theloop portion is between the ECL luminophore and the functional moiety.

Preferably, the CMOS circuitry is configured to provide an electricalpulse to the electrodes.

Preferably, the electrical pulse has a duration less than 0.69 seconds.

Preferably, the electrical pulse has a current of 0.1 nanoamperes to69.0 nanoamperes.

Preferably, the electrodes have an anode and a cathode each havingfingers configured such that the fingers of the anode are interdigitatedwith the fingers of the cathode.

Preferably, the anode and the cathode are separated by a dielectric gapbetween 0.4 microns and 2 microns wide.

Preferably, the transparent wall section is less than 1600 micronsthick.

Preferably, the photosensor is an array of photodiodes positioned inregistration with the hybridization chambers such that each of thehybridization chambers corresponds to one of the photodiodesrespectively.

Preferably, the photodiodes each have a planar active surface area suchthat the planar active surface areas collectively provide the collectionsurface, each of the active surface areas being coplanar, and theelectrodes are a layer of conductive material patterned to form theseparate anodes and cathodes, the layer extending in a plane parallel tothat of the active surface areas of the photodiodes.

Preferably, one of the electrodes in each of the electrode pairs is aworking electrode which causes oxidation or reduction of the luminophoreto generate an excited species that emits a photon, the workingelectrode being positioned such that the probes are between thephotodiode and the working electrode.

Preferably, the luminophore is a metalorganic complex.

Preferably, the metalorganic complex is a ruthenium organic complexmolecule.

Preferably, the LOC device also has a dialysis section for diverting thecells smaller than a predetermined size threshold into a separatestream.

The easily usable, mass-producible, inexpensive, compact, and light LOCdevice accepts a biological sample, amplifies the nucleic acid targetsin the sample, identifies the sample's nucleic acid sequences viahybridization with electrochemiluminescence resonance energy transferprimer-linked stem-and-loop probes using its integral image sensor, andprovides the results electronically at its output pads, with theprimer-linked stem-and-loop probes providing for a large number ofoptimal parallel amplification reactions to be run, also providing forhigh specificity, sensitivity, and reliability of detection of thetarget sequences.

The electrochemiluminescence-based assay target detection obviates anyneed, of the assay system, for an excitation light source, excitationoptics, and optical filter elements, in turn, providing for a morecompact and more inexpensive assay system. The absence of therequirement for the rejection of any excitation light also simplifiesthe detector circuitry, making the assay system even more inexpensive.

BRIEF DESCRIPTION OF THE DRAWINGS

Preferred embodiments of the present invention will now be described byway of example only with reference to the accompanying drawings, inwhich:

FIG. 1 shows a test module and test module reader configured forfluorescence detection;

FIG. 2 is a schematic overview of the electronic components in the testmodule configured for fluorescence detection;

FIG. 3 is a schematic overview of the electronic components in the testmodule reader;

FIG. 4 is a schematic representation of the architecture of the LOCdevice;

FIG. 5 is a perspective of the LOC device;

FIG. 6 is a plan view of the LOC device with features and structuresfrom all layers superimposed on each other;

FIG. 7 is a plan view of the LOC device with the structures of the capshown in isolation;

FIG. 8 is a top perspective of the cap with internal channels andreservoirs shown in dotted line;

FIG. 9 is an exploded top perspective of the cap with internal channelsand reservoirs shown in dotted line;

FIG. 10 is a bottom perspective of the cap showing the configuration ofthe top channels;

FIG. 11 is a plan view of the LOC device showing the structures of theCMOS +MST device in isolation;

FIG. 12 is a schematic section view of the LOC device at the sampleinlet;

FIG. 13 is an enlarged view of Inset AA shown in FIG. 6;

FIG. 14 is an enlarged view of Inset AB shown in FIG. 6;

FIG. 15 is an enlarged view of Inset AE shown in FIG. 13;

FIG. 16 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 17 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 18 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 19 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 20 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 21 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AE;

FIG. 22 is schematic section view of the lysis reagent reservoir shownin FIG. 21;

FIG. 23 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 24 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 25 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AI;

FIG. 26 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 27 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 28 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 29 is a partial perspective illustrating the laminar structure ofthe LOC device within Inset AB;

FIG. 30 is a schematic section view of the amplification mix reservoirand the polymerase reservoir;

FIG. 31 show the features of a boiling-initiated valve in isolation;

FIG. 32 is a schematic section view of the boiling-initiated valve takenthrough line 33-33 shown in FIG. 31;

FIG. 33 is an enlarged view of Inset AF shown in FIG. 15;

FIG. 34 is a schematic section view of the upstream end of the dialysissection taken through line 35-35 shown in FIG. 33;

FIG. 35 is an enlarged view of Inset AC shown in FIG. 6;

FIG. 36 is a further enlarged view within Inset AC showing theamplification section;

FIG. 37 is a further enlarged view within Inset AC showing theamplification section;

FIG. 38 is a further enlarged view within Inset AC showing theamplification section;

FIG. 39 is a further enlarged view within Inset AK shown in FIG. 38;

FIG. 40 is a further enlarged view within Inset AC showing theamplification chamber;

FIG. 41 is a further enlarged view within Inset AC showing theamplification section;

FIG. 42 is a further enlarged view within Inset AC showing theamplification chamber;

FIG. 43 is a further enlarged view within Inset AL shown in FIG. 42;

FIG. 44 is a further enlarged view within Inset AC showing theamplification section;

FIG. 45 is a further enlarged view within Inset AM shown in FIG. 44;

FIG. 46 is a further enlarged view within Inset AC showing theamplification chamber;

FIG. 47 is a further enlarged view within Inset AN shown in FIG. 46;

FIG. 48 is a further enlarged view within Inset AC showing theamplification chamber;

FIG. 49 is a further enlarged view within Inset AC showing theamplification chamber;

FIG. 50 is a further enlarged view within Inset AC showing theamplification section;

FIG. 51 is a schematic section view of the amplification section;

FIG. 52 is an enlarged plan view of the hybridization section;

FIG. 53 is a further enlarged plan view of two hybridization chambers inisolation;

FIG. 54 is schematic section view of a single hybridization chamber;

FIG. 55 is an enlarged view of the humidifier illustrated in Inset AGshown in FIG. 6;

FIG. 56 is an enlarged view of Inset AD shown in FIG. 52;

FIG. 57 is an exploded perspective view of the LOC device within InsetAD;

FIG. 58 is an enlarged plan view of the humidity sensor shown in InsetAH of FIG. 6;

FIG. 59 is a schematic section view of a leukocyte target dialysissection;

FIG. 60 is a schematic showing part of the photodiode array of the photosensor;

FIG. 61 is an enlarged view of the evaporator shown in Inset AP of FIG.55;

FIG. 62 is a diagram of linker-primed PCR;

FIG. 63 is a schematic representation of a test module with a lancet;

FIG. 64 is a diagrammatic representation of the architecture of LOCvariant VII;

FIG. 65 is a plan view of LOC variant VIII with features and structuresfrom all layers superimposed on each other;

FIG. 66 is an enlarged view of Inset CA shown in FIG. 65;

FIG. 67 is a partial perspective illustrating the laminar structure ofLOC variant VIII within Inset CA shown in FIG. 65;

FIG. 68 is an enlarged view of Inset CE shown in FIG. 66;

FIG. 69 is a diagrammatic representation of the architecture of LOCvariant VIII;

FIG. 70 is a schematic illustration of the architecture of LOC variantXIV;

FIG. 71 is a schematic illustration of the architecture of LOC variantXLI;

FIG. 72 is a schematic illustration of the architecture of LOC variantXLII;

FIG. 73 is a schematic illustration of the architecture of LOC variantXLIII;

FIG. 74 is a schematic illustration of the architecture of LOC variantXLIV;

FIG. 75 is a schematic illustration of the architecture of LOC variantXLVII;

FIG. 76 is a diagrammatic representation of the architecture of LOCvariant X;

FIG. 77 is a perspective view of LOC variant X;

FIG. 78 is a plan view of LOC variant X showing the structures of theCMOS+MST device in isolation;

FIG. 79 is a perspective view of the underside of the cap with thereagent reservoirs shown in dotted line;

FIG. 80 is a plan view showing only the features of the cap inisolation;

FIG. 81 is a plan view showing all the features superimposed on eachother, and showing the location of Insets DA to DK;

FIG. 82 is an enlarged view of Inset DA shown in FIG. 81;

FIG. 83 is an enlarged view of Inset DB shown in FIG. 81;

FIG. 84 is an enlarged view of Inset DC shown in FIG. 81;

FIG. 85 is an enlarged view of Inset DD shown in FIG. 81;

FIG. 86 is an enlarged view of Inset DE shown in FIG. 81;

FIG. 87 is an enlarged view of Inset DF shown in FIG. 81;

FIG. 88 is an enlarged view of Inset DG shown in FIG. 81;

FIG. 89 is an enlarged view of Inset DH shown in FIG. 81;

FIG. 90 is an enlarged view of Inset DJ shown in FIG. 81;

FIG. 91 is an enlarged view of Inset DK shown in FIG. 81;

FIG. 92 is an enlarged view of Inset DL shown in FIG. 81;

FIG. 93 is a circuit diagram of the differential imager;

FIG. 94 schematically illustrates a CMOS-controlled flow rate sensor;

FIG. 95 illustrates the reactions occurring during anelectrochemiluminescence (ECL) process;

FIG. 96 schematically illustrates three different anode configurations;

FIG. 97 is a schematic partial cross-section of the anode and cathode inthe hybridization chamber;

FIG. 98 schematically illustrates an anode in a ring geometry around theperipheral edge of a photodiode;

FIG. 99 schematically illustrates an anode in a ring geometry within theperipheral edge of a photodiode;

FIG. 100 schematically illustrates an anode with a series of fingers toincrease the length of its lateral edges;

FIG. 101 schematically illustrates the use of a transparent anode tomaximise surface area coupling and ECL signal detection;

FIG. 102 schematically illustrates the use of an anode affixed to theroof of the hybridization chamber to maximise surface area coupling andECL signal detection;

FIG. 103 schematically illustrates an anode interdigitated with acathode;

FIG. 104 shows a test module and test module reader configured for usewith ECL detection;

FIG. 105 is a schematic overview of the electronic components in thetest module configured for use with ECL detection;

FIG. 106 shows a test module and alternative test module readers;

FIG. 107 shows a test module and test module reader along with thehosting system housing various databases;

FIGS. 108A and 108B is a diagram illustrating binding of an aptamer to aprotein to produce a detectable signal;

FIGS. 109A and 109B are diagrams illustrating binding of two aptamers toa protein to produce a detectable signal;

FIGS. 110A and 110B are diagrams illustrating binding of two antibodiesto a protein to produce a detectable signal;

FIG. 111 is a diagrammatic representation of the architecture of LOCvariant L with ECL detection;

FIG. 112 is a perspective view of LOC variant L;

FIG. 113 is a plan view of LOC variant L showing the structures of theCMOS+MST device in isolation;

FIG. 114 is a perspective view of the underside of the cap of LOCvariant L with the reagent reservoirs shown in dotted lines;

FIG. 115 is a plan view of LOC variant L showing the features of the capin isolation;

FIG. 116 is a plan view of LOC variant L showing all the featuressuperimposed on each other and showing the locations of Insets GA to GL;

FIG. 117 is an enlarged view of Inset GA shown in FIG. 116;

FIG. 118 is an enlarged view of Inset GB shown in FIG. 116;

FIG. 119 is an enlarged view of Inset GC shown in FIG. 116;

FIG. 120 is an enlarged view of Inset GD shown in FIG. 116;

FIG. 121 is an enlarged view of Inset GE shown in FIG. 116;

FIG. 122 is an enlarged view of Inset GF shown in FIG. 116;

FIG. 123 is an enlarged view of Inset GG shown in FIG. 116;

FIG. 124 is an enlarged view of Inset GH shown in FIG. 116;

FIG. 125 is an enlarged view of Inset GJ shown in FIG. 116;

FIG. 126 is an enlarged view of Inset GK shown in FIG. 116;

FIG. 127 is an enlarged view of Inset GL shown in FIG. 116;

FIG. 128 is a diagrammatic representation of a LOC device with thermalinsulation trench;

FIG. 129 is a diagram of an electrochemiluminescence resonance energytransfer probe in a closed configuration;

FIG. 130 is a diagram of an electrochemiluminescence resonance energytransfer probe in an open and hybridized configuration;

FIG. 131 is a diagram of a primer-linked, luminescent linear probeduring the initial round of amplification;

FIG. 132 is a diagram of a primer-linked, luminescent linear probeduring a subsequent amplification cycle;

FIGS. 133A to 133F diagrammatically illustrate thermal cycling of aluminescent primer-linked stem-and-loop probe;

FIG. 134 schematically illustrates a negative control luminescent probein its stem-and-loop configuration;

FIG. 135 schematically illustrates the negative control luminescentprobe of FIG. 134 in its open configuration;

FIG. 136 schematically illustrates a positive control luminescent probein its stem-and-loop configuration;

FIG. 137 schematically illustrates the positive control luminescentprobe of FIG. 136 in its open configuration;

FIG. 138 is an enlarged view of the hybridization chamber of LOC variantL;

FIG. 139 is an enlarged view of the hybridization chamber array of LOCvariant L showing the distribution of calibration chambers;

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Overview

This overview identifies the main components of a molecular diagnosticsystem that incorporates embodiments of the present invention.Comprehensive details of the system architecture and operation are setout later in the specification.

Referring to FIGS. 1, 2, 3, 104 and 105, the system has the followingtop level components:

Test modules 10 and 11 are the size of a typical USB memory key and verycheap to produce. Test modules 10 and 11 each contain a microfluidicdevice, typically in the form of a lab-on-a-chip (LOC) device 30preloaded with reagents and typically more than 1000 probes for themolecular diagnostic assay (see FIGS. 1 and 104). Test module 10schematically shown in FIG. 1 uses a fluorescence-based detectiontechnique to identify target molecules, while test module 11 in FIG. 104uses an electrochemiluminescence-based detection technique. The LOCdevice 30 has an integrated photosensor 44 for fluorescence orelectrochemiluminescence detection (described in detail below). Bothtest modules 10 and 11 use a standard Micro-USB plug 14 for power, dataand control, both have a printed circuit board (PCB) 57, and both haveexternal power supply capacitors 32 and an inductor 15. The test modules10 and 11 are both single-use only for mass production and distributionin sterile packaging ready for use.

The outer casing 13 has a macroreceptacle 24 for receiving thebiological sample and a removable sterile sealing tape 22, preferablywith a low tack adhesive, to cover the macroreceptacle prior to use. Amembrane seal 408 with a membrane guard 410 forms part of the outercasing 13 to reduce dehumidification within the test module whileproviding pressure relief from small air pressure fluctuations. Themembrane guard 410 protects the membrane seal 408 from damage.

Test module reader 12 powers the test module 10 or 11 via Micro-USB port16. The test module reader 12 can adopt many different forms and aselection of these are described later. The version of the reader 12shown in FIGS. 1, 3 and 104 is a smart phone embodiment. A block diagramof this reader 12 is shown in FIG. 3. Processor 42 runs applicationsoftware from program storage 43. The processor 42 also interfaces withthe display screen 18 and user interface (UI) touch screen 17 andbuttons 19, a cellular radio 21, wireless network connection 23, and asatellite navigation system 25. The cellular radio 21 and wirelessnetwork connection 23 are used for communications. Satellite navigationsystem 25 is used for updating epidemiological databases with locationdata. The location data can, alternatively, be entered manually via thetouch screen 17 or buttons 19. Data storage 27 holds genetic anddiagnostic information, test results, patient information, assay andprobe data for identifying each probe and its array position. Datastorage 27 and program storage 43 may be shared in a common memoryfacility. Application software installed on the test module reader 12provides analysis of results, along with additional test and diagnosticinformation.

To conduct a diagnostic test, the test module 10 (or test module 11) isinserted into the Micro-USB port 16 on the test module reader 12. Thesterile sealing tape 22 is peeled back and the biological sample (in aliquid form) is loaded into the sample macroreceptacle 24. Pressingstart button 20 initiates testing via the application software. Thesample flows into the LOC device 30 and the on-board assay extracts,incubates, amplifies and hybridizes the sample nucleic acids (thetarget) with presynthesized hybridization-responsive oligonucleotideprobes. In the case of test module 10 (which uses fluorescence-baseddetection), the probes are fluorescently labelled and the LED 26 housedin the casing 13 provides the necessary excitation light to inducefluorescence emission from the hybridized probes (see FIGS. 1 and 2). Intest module 11 (which uses electrochemiluminescence (ECL) detection),the LOC device 30 is loaded with ECL probes (discussed above) and theLED 26 is not necessary for generating the luminescent emission.Instead, electrodes 860 and 870 provide the excitation electricalcurrent (see FIG. 105). The emission (fluorescent or luminescent) isdetected using a photosensor 44 integrated into CMOS circuitry of eachLOC device. The detected signal is amplified and converted to a digitaloutput which is analyzed by the test module reader 12. The reader thendisplays the results.

The data may be saved locally and/or uploaded to a network servercontaining patient records. The test module 10 or 11 is removed from thetest module reader 12 and disposed of appropriately.

FIGS. 1, 3 and 104 show the test module reader 12 configured as a mobilephone/smart phone 28. In other forms, the test module reader is alaptop/notebook 101, a dedicated reader 103, an ebook reader 107, atablet computer 109 or desktop computer 105 for use in hospitals,private practices or laboratories (see FIG. 106). The reader caninterface with a range of additional applications such as patientrecords, billing, online databases and multi-user environments. It canalso be interfaced with a range of local or remote peripherals such asprinters and patient smart cards.

Referring to FIG. 107, the data generated by the test module 10 can beused to update, via the reader 12 and network 125, the epidemiologicaldatabases hosted on the hosting system for epidemiological data 111, thegenetic databases hosted on the hosting system for genetic data 113, theelectronic health records hosted on the hosting system for electronichealth records (EHR) 115, the electronic medical records hosted on thehosting system for electronic medical records (EMR) 121, and thepersonal health records hosted on the hosting system for personal healthrecords (PHR) 123. Conversely, the epidemiological data hosted on thehosting system for epidemiological data 111, the genetic data hosted onthe hosting system for genetic data 113, the electronic health recordshosted on the hosting system for electronic health records (EHR) 115,the electronic medical records hosted on the hosting system forelectronic medical records (EMR) 121, and the personal health recordshosted on the hosting system for personal health records (PHR) 123, canbe used to update, via network 125 and the reader 12, the digital memoryin the LOC 30 of the test module 10.

Referring back to FIGS. 1, 2, 104 and 105 the reader 12 uses batterypower in the mobile phone configuration. The mobile phone readercontains all test and diagnostic information preloaded. Data can also beloaded or updated via a number of wireless or contact interfaces toenable communications with peripheral devices, computers or onlineservers. A Micro-USB port 16 is provided for connection to a computer ormains power supply for battery recharge.

FIG. 63 shows an embodiment of the test module 10 used for tests thatonly require a positive or negative result for a particular target, suchas testing whether a person is infected with, for example, H1N1Influenza A virus. Only a purpose built USB power/indicator-only module47 is adequate. No other reader or application software is necessary. Anindicator 45 on the USB power/indicator-only module 47 signals positiveor negative results. This configuration is well suited to massscreening.

Additional items supplied with the system may include a test tubecontaining reagents for pre-treatment of certain samples, along withspatula and lancet for sample collection. FIG. 63 shows an embodiment ofthe test module incorporating a spring-loaded, retractable lancet 390and lancet release button 392 for convenience. A satellite phone can beused in remote areas.

Test Module Electronics

FIGS. 2 and 105 are block diagrams of the electronic components in thetest modules 10 and 11, respectively. The CMOS circuitry integrated inthe LOC device 30 has a USB device driver 36, a controller 34, aUSB-compatible LED driver 29, clock 33, power conditioner 31, RAM 38 andprogram and data flash memory 40. These provide the control and memoryfor the entire test module 10 or 11 including the photosensor 44, thetemperature sensors 170, the liquid sensors 174, and the various heaters152, 154, 182, 234, together with associated drivers 37 and 39 andregisters 35 and 41. Only the LED 26 (in the case of test module 10),external power supply capacitors 32 and the Micro-USB plug 14 areexternal to the LOC device 30. The LOC devices 30 include bond-pads formaking connections to these external components. The RAM 38 and theprogram and data flash memory 40 have the application software and thediagnostic and test information (Flash/Secure storage, e.g. viaencryption) for over 1000 probes. In the case of test module 11configured for ECL detection, there is no LED 26 (see FIGS. 104 and105). Data is encrypted by the LOC device 30 for secure storage andsecure communication with an external device. The LOC devices 30 areloaded with electrochemiluminescent probes and the hybridizationchambers each have a pair of ECL excitation electrodes 860 and 870.

Many types of test modules 10 are manufactured in a number of testforms, ready for off-the-shelf use. The differences between the testforms lie in the on board assay of reagents and probes.

Some examples of infectious diseases rapidly identified with this systeminclude:

-   -   Influenza—Influenza virus A, B, C, Isavirus, Thogotovirus    -   Pneumonia—respiratory syncytial virus (RSV), adenovirus,        metapneumovirus, Streptococcus pneumoniae, Staphylococcus aureus    -   Tuberculosis—Mycobacterium tuberculosis, bovis, africanum,        canetti, and microti    -   Plasmodium falciparum, Toxoplasma gondii and other protozoan        parasites    -   Typhoid—Salmonella enterica serovar typhi    -   Ebola virus    -   Human immunodeficiency virus (HIV)    -   Dengue Fever—Flavivirus    -   Hepatitis (A through E)    -   Hospital acquired infections—for example Clostridium difficile,        Vancomycin resistant Enterococcus, and Methicillin resistant        Staphylococcus aureus    -   Herpes simplex virus (HSV)    -   Cytomegalovirus (CMV)    -   Epstein-Barr virus (EBV)    -   Encephalitis—Japanese Encephalitis virus, Chandipura virus    -   Whooping cough—Bordetella pertussis    -   Measles—paramyxovirus    -   Meningitis—Streptococcus pneumoniae and Neisseria meningitidis    -   Anthrax—Bacillus anthracis

Some examples of genetic disorders identified with this system include:

-   -   Cystic fibrosis    -   Haemophilia    -   Sickle cell disease    -   Tay-Sachs disease    -   Haemochromatosis    -   Cerebral arteriopathy    -   Crohn's disease    -   Polycistic kidney disease    -   Congential heart disease    -   Rett syndrome

A small selection of cancers identified by the diagnostic systeminclude:

-   -   Ovarian    -   Colon carcinoma    -   Multiple endocrine neoplasia    -   Retinoblastoma    -   Turcot syndrome

The above lists are not exhaustive and the diagnostic system can beconfigured to detect a much greater variety of diseases and conditionsusing nucleic acid and proteomic analysis.

Detailed Architecture of System Components LOC Device

The LOC device 30 is central to the diagnostic system. It rapidlyperforms the four major steps of a nucleic acid based moleculardiagnostic assay, i.e. sample preparation, nucleic acid extraction,nucleic acid amplification, and detection, using a microfluidicplatform. The LOC device also has alternative uses, and these aredetailed later. As discussed above, test modules 10 and 11 can adoptmany different configurations to detect different targets Likewise, theLOC device 30 has numerous different embodiments tailored to thetarget(s) of interest. One form of the LOC device 30 is LOC device 301for fluorescent detection of target nucleic acid sequences in thepathogens of a whole blood sample. For the purposes of illustration, thestructure and operation of LOC device 301 is now described in detailwith reference to FIGS. 4 to 26 and 27 to 57.

FIG. 4 is a schematic representation of the architecture of the LOCdevice 301. For convenience, process stages shown in FIG. 4 areindicated with the reference numeral corresponding to the functionalsections of the LOC device 301 that perform that process stage. Theprocess stages associated with each of the major steps of a nucleic acidbased molecular diagnostic assay are also indicated: sample input andpreparation 288, extraction 290, incubation 291, amplification 292 anddetection 294. The various reservoirs, chambers, valves and othercomponents of the LOC device 301 will be described in more detail later.

FIG. 5 is a perspective view of the LOC device 301. It is fabricatedusing high volume CMOS and MST (microsystems technology) manufacturingtechniques. The laminar structure of the LOC device 301 is illustratedin the schematic (not to scale) partial section view of FIG. 12. The LOCdevice 301 has a silicon substrate 84 which supports the CMOS+MST chip48, comprising CMOS circuitry 86 and an MST layer 87, with a cap 46overlaying the MST layer 87. For the purposes of this patentspecification, the term ‘MST layer’ is a reference to a collection ofstructures and layers that process the sample with various reagents.Accordingly, these structures and components are configured to defineflow-paths with characteristic dimensions that will support capillarydriven flow of liquids with physical characteristics similar to those ofthe sample during processing. In light of this, the MST layer andcomponents are typically fabricated using surface micromachiningtechniques and/or bulk micromachining techniques. However, otherfabrication methods can also produce structures and componentsdimensioned for capillary driven flows and processing very smallvolumes. The specific embodiments described in this specification showthe MST layer as the structures and active components supported on theCMOS circuitry 86, but excluding the features of the cap 46. However,the skilled addressee will appreciate that the MST layer need not haveunderlying CMOS or indeed an overlying cap in order for it to processthe sample.

The overall dimensions of the LOC device shown in the following figuresare 1760 μm×5824 μm. Of course, LOC devices fabricated for differentapplications may have different dimensions.

FIG. 6 shows the features of the MST layer 87 superimposed with thefeatures of the cap. Insets AA to AD, AG and AH shown in FIG. 6 areenlarged in FIGS. 13, 14, 35, 56, 55 and 58, respectively, and describedin detail below for a comprehensive understanding of each structurewithin the LOC device 301. FIGS. 7 to 10 show the features of the cap 46in isolation while FIG. 11 shows the CMOS +MST device 48 structures inisolation.

Laminar Structure

FIGS. 12 and 22 are sketches that diagrammatically show the laminarstructure of the CMOS+MST device 48, the cap 46 and the fluidicinteraction between the two. The figures are not to scale for thepurposes of illustration. FIG. 12 is a schematic section view throughthe sample inlet 68 and FIG. 22 is a schematic section through thereservoir 54. As best shown in FIG. 12, the CMOS+MST device 48 has asilicon substrate 84 which supports the CMOS circuitry 86 that operatesthe active elements within the MST layer 87 above. A passivation layer88 seals and protects the CMOS layer 86 from the fluid flows through theMST layer 87.

Fluid flows through both the cap channels 94 and the MST channels 90(see for example FIGS. 7 and 16) in the cap layer 46 and MST channellayer 100, respectively. Cell transport occurs in the larger channels 94fabricated in the cap 46, while biochemical processes are carried out inthe smaller MST channels 90. Cell transport channels are sized so as tobe able to transport cells in the sample to predetermined sites in theMST channels 90. Transportation of cells with sizes greater than 20microns (for example, certain leukocytes) requires channel dimensionsgreater than 20 microns, and therefore a cross sectional area transverseto the flow of greater than 400 square microns. MST channels,particularly at locations in the LOC where transport of cells is notrequired, can be significantly smaller.

It will be appreciated that cap channel 94 and MST channel 90 aregeneric references and particular MST channels 90 may also be referredto as (for example) heated microchannels or dialysis MST channels inlight of their particular function. MST channels 90 are formed byetching through a MST channel layer 100 deposited on the passivationlayer 88 and patterned with photoresist. The MST channels 90 areenclosed by a roof layer 66 which forms the top (with respect to theorientation shown in the figures) of the CMOS+MST device 48.

Despite sometimes being shown as separate layers, the cap channel layer80 and the reservoir layer 78 are formed from a unitary piece ofmaterial. Of course, the piece of material may also be non-unitary. Thispiece of material is etched from both sides in order to form a capchannel layer 80 in which the cap channels 94 are etched and thereservoir layer 78 in which the reservoirs 54, 56, 58, 60 and 62 areetched. Alternatively, the reservoirs and the cap channels are formed bya micromolding process. Both etching and micromolding techniques areused to produce channels with cross sectional areas transverse to theflow as large as 20,000 square microns, and as small as 8 squaremicrons.

At different locations in the LOC device, there can be a range ofappropriate choices for the cross sectional area of the channeltransverse to the flow. Where large quantities of sample, or sampleswith large constituents, are contained in the channel, a cross-sectionalarea of up to 20,000 square microns (for example, a 200 micron widechannel in a 100 micron thick layer) is suitable. Where small quantitiesof liquid, or mixtures without large cells present, are contained in thechannel, a very small cross sectional area transverse to the flow ispreferable.

A lower seal 64 encloses the cap channels 94 and the upper seal layer 82encloses the reservoirs 54, 56, 58, 60 and 62.

The five reservoirs 54, 56, 58, 60 and 62 are preloaded withassay-specific reagents. In the embodiment described here, thereservoirs are preloaded with the following reagents, but other reagentscan easily be substituted:

-   -   reservoir 54: anticoagulant with option to include erythrocyte        lysis buffer    -   reservoir 56: lysis reagent    -   reservoir 58: restriction enzymes, ligase and linkers (for        linker-primed PCR (see FIG. 62, extracted from T. Stachan et        al., Human Molecular Genetics 2, Garland Science, NY and London,        1999))    -   reservoir 60: amplification mix (dNTPs, primers, buffer) and    -   reservoir 62: DNA polymerase.

The cap 46 and the CMOS+MST layers 48 are in fluid communication viacorresponding openings in the lower seal 64 and the roof layer 66. Theseopenings are referred to as uptakes 96 and downtakes 92 depending onwhether fluid is flowing from the MST channels 90 to the cap channels 94or vice versa.

LOC Device Operation

The operation of the LOC device 301 is described below in a step-wisefashion with reference to analysing pathogenic DNA in a blood sample. Ofcourse, other types of biological or non-biological fluid are alsoanalysed using an appropriate set, or combination, of reagents, testprotocols, LOC variants and detection systems. Referring back to FIG. 4,there are five major steps involved in analysing a biological sample,comprising sample input and preparation 288, nucleic acid extraction290, nucleic acid incubation 291, nucleic acid amplification 292 anddetection and analysis 294.

The sample input and preparation step 288 involves mixing the blood withan anticoagulant 116 and then separating pathogens from the leukocytesand erythrocytes with the pathogen dialysis section 70. As best shown inFIGS. 7 and 12, the blood sample enters the device via the sample inlet68. Capillary action draws the blood sample along the cap channel 94 tothe reservoir 54. Anticoagulant is released from the reservoir 54 as thesample blood flow opens its surface tension valve 118 (see FIGS. 15 and22). The anticoagulant prevents the formation of clots which would blockthe flow.

As best shown in FIG. 22, the anticoagulant 116 is drawn out of thereservoir 54 by capillary action and into the MST channel 90 via thedowntake 92. The downtake 92 has a capillary initiation feature (CIF)102 to shape the geometry of the meniscus such that it does not anchorto the rim of the downtake 92. Vent holes 122 in the upper seal 82allows air to replace the anticoagulant 116 as it is drawn out of thereservoir 54.

The MST channel 90 shown in FIG. 22 is part of a surface tension valve118. The anticoagulant 116 fills the surface tension valve 118 and pinsa meniscus 120 to the uptake 96 to a meniscus anchor 98. Prior to use,the meniscus 120 remains pinned at the uptake 96 so the anticoagulantdoes not flow into the cap channel 94. When the blood flows through thecap channel 94 to the uptake 96, the meniscus 120 is removed and theanticoagulant is drawn into the flow.

FIGS. 15 to 21 show Inset AE which is a portion of Inset AA shown inFIG. 13. As shown in FIGS. 15, 16 and 17, the surface tension valve 118has three separate MST channels 90 extending between respectivedowntakes 92 and uptakes 96. The number of MST channels 90 in a surfacetension valve can be varied to change the flow rate of the reagent intothe sample mixture. As the sample mixture and the reagents mix togetherby diffusion, the flow rate out of the reservoir determines theconcentration of the reagent in the sample flow. Hence, the surfacetension valve for each of the reservoirs is configured to match thedesired reagent concentration.

The blood passes into a pathogen dialysis section 70 (see FIGS. 4 and15) where target cells are concentrated from the sample using an arrayof apertures 164 sized according to a predetermined threshold. Cellssmaller than the threshold pass through the apertures while larger cellsdo not pass through the apertures. Unwanted cells, which may be eitherthe larger cells withheld by the array of apertures 164 or the smallercells that pass through the apertures, are redirected to a waste unit 76while the target cells continue as part of the assay.

In the pathogen dialysis section 70 described here, the pathogens fromthe whole blood sample are concentrated for microbial DNA analysis. Thearray of apertures is formed by a multitude of 3 micron diameter holes164 fluidically connecting the input flow in the cap channel 94 to atarget channel 74. The 3 micron diameter apertures 164 and the dialysisuptake holes 168 for the target channel 74 are connected by a series ofdialysis MST channels 204 (best shown in FIGS. 15 and 21). Pathogens aresmall enough to pass through the 3 micron diameter apertures 164 andfill the target channel 74 via the dialysis MST channels 204. Cellslarger than 3 microns, such as erythrocytes and leukocytes, stay in thewaste channel 72 in the cap 46 which leads to a waste reservoir 76 (seeFIG. 7).

Other aperture shapes, sizes and aspect ratios can be used to isolatespecific pathogens or other target cells such as leukocytes for humanDNA analysis. Greater detail on the dialysis section and dialysisvariants is provided later.

Referring again to FIGS. 6 and 7, the flow is drawn through the targetchannel 74 to the surface tension valve 128 of the lysis reagentreservoir 56. The surface tension valve 128 has seven MST channels 90extending between the lysis reagent reservoir 56 and the target channel74. When the menisci are unpinned by the sample flow, the flow rate fromall seven of the MST channels 90 will be greater than the flow rate fromthe anticoagulant reservoir 54 where the surface tension valve 118 hasthree MST channels 90 (assuming the physical characteristics of thefluids are roughly equivalent). Hence the proportion of lysis reagent inthe sample mixture is greater than that of the anticoagulant.

The lysis reagent and target cells mix by diffusion in the targetchannel 74 within the chemical lysis section 130. A boiling-initiatedvalve 126 stops the flow until sufficient time has passed for diffusionand lysis to take place, releasing the genetic material from the targetcells (see FIGS. 6 and 7). The structure and operation of theboiling-initiated valves are described in greater detail below withreference to FIGS. 31 and 32. Other active valve types (as opposed topassive valves such as the surface tension valve 118) have also beendeveloped by the Applicant which may be used here instead of theboiling-initiated valve. These alternative valve designs are alsodescribed later.

When the boiling-initiated valve 126 opens, the lysed cells flow into amixing section 131 for pre-amplification restriction digestion andlinker ligation.

Referring to FIG. 13, restriction enzymes, linkers and ligase arereleased from the reservoir 58 when the flow unpins the menisci at thesurface tension valve 132 at the start of the mixing section 131. Themixture flows the length of the mixing section 131 for diffusion mixing.At the end of the mixing section 131 is downtake 134 leading into theincubator inlet channel 133 of the incubation section 114 (see FIG. 13).The incubator inlet channel 133 feeds the mixture into a serpentineconfiguration of heated microchannels 210 which provides an incubationchamber for holding the sample during restriction digestion and ligationof the linkers (see FIGS. 13 and 14).

FIGS. 23, 24, 25, 26, 27, 28 and 29 show the layers of the LOC device301 within Inset AB of FIG. 6. Each figure shows the sequential additionof layers forming the structures of the CMOS+MST layer 48 and the cap46. Inset AB shows the end of the incubation section 114 and the startof the amplification section 112. As best shown in FIGS. 14 and 23, theflow fills the microchannels 210 of the incubation section 114 untilreaching the boiling-initiated valve 106 where the flow stops whilediffusion takes place. As discussed above, the microchannel 210 upstreamof the boiling-initiated valve 106 becomes an incubation chambercontaining the sample, restriction enzymes, ligase and linkers. Theheaters 154 are then activated and held at constant temperature for aspecified time for restriction digestion and linker ligation to occur.

The skilled worker will appreciate that this incubation step 291 (seeFIG. 4) is optional and only required for some nucleic acidamplification assay types. Furthermore, in some instances, it may benecessary to have a heating step at the end of the incubation period tospike the temperature above the incubation temperature. The temperaturespike inactivates the restriction enzymes and ligase prior to enteringthe amplification section 112. Inactivation of the restriction enzymesand ligase has particular relevance when isothermal nucleic acidamplification is being employed.

Following incubation, the boiling-initiated valve 106 is activated(opened) and the flow resumes into the amplification section 112.Referring to FIGS. 31 and 32, the mixture fills the serpentineconfiguration of heated microchannels 158, which form one or moreamplification chambers, until it reaches the boiling-initiated valve108. As best shown in the schematic section view of FIG. 30,amplification mix (dNTPs, primers, buffer) is released from reservoir 60and polymerase is subsequently released from reservoir 62 into theintermediate MST channel 212 connecting the incubation and amplificationsections (114 and 112 respectively).

FIGS. 35 to 51 show the layers of the LOC device 301 within Inset AC ofFIG. 6. Each figure shows the sequential addition of layers forming thestructures of the CMOS+MST device 48 and the cap 46. Inset AC is at theend of the amplification section 112 and the start of the hybridizationand detection section 52. The incubated sample, amplification mix andpolymerase flow through the microchannels 158 to the boiling-initiatedvalve 108. After sufficient time for diffusion mixing, the heaters 154in the microchannels 158 are activated for thermal cycling or isothermalamplification. The amplification mix goes through a predetermined numberof thermal cycles or a preset amplification time to amplify sufficienttarget DNA. After the nucleic acid amplification process, theboiling-initiated valve 108 opens and flow resumes into thehybridization and detection section 52. The operation ofboiling-initiated valves is described in more detail later.

As shown in FIG. 52, the hybridization and detection section 52 has anarray of hybridization chambers 110. FIGS. 52, 53, 54 and 56 show thehybridization chamber array 110 and individual hybridization chambers180 in detail. At the entrance to the hybridization chamber 180 is adiffusion barrier 175 which prevents diffusion of the target nucleicacid, probe strands and hybridized probes between the hybridizationchambers 180 during hybridization so as to prevent erroneoushybridization detection results. The diffusion barriers 175 present aflow-path-length that is long enough to prevent the target sequences andprobes diffusing out of one chamber and contaminating another chamberwithin the time taken for the probes and nucleic acids to hybridize andthe signal to be detected, thus avoiding an erroneous result.

Another mechanism to prevent erroneous readings is to have identicalprobes in a number of the hybridization chambers. The CMOS circuitry 86derives a single result from the photodiodes 184 corresponding to thehybridization chambers 180 that contain identical probes. Anomalousresults can be disregarded or weighted differently in the derivation ofthe single result.

The thermal energy required for hybridization is provided byCMOS-controlled heaters 182 (described in more detail below). After theheater is activated, hybridization occurs between complementarytarget-probe sequences. The LED driver 29 in the CMOS circuitry 86signals the LED 26 located in the test module 10 to illuminate. Theseprobes only fluoresce when hybridization has occurred thereby avoidingwashing and drying steps that are typically required to remove unboundstrands. Hybridization forces the stem-and-loop structure of the FRETprobes 186 to open, which allows the fluorophore to emit fluorescentenergy in response to the LED excitation light, as discussed in greaterdetail later. Fluorescence is detected by a photodiode 184 in the CMOScircuitry 86 underlying each hybridization chamber 180 (seehybridization chamber description below). The photodiodes 184 for allhybridization chambers and associated electronics collectively form thephotosensor 44 (see FIG. 60). In other embodiments, the photosensor maybe an array of charge coupled devices (CCD array). The detected signalfrom the photodiodes 184 is amplified and converted to a digital outputwhich is analyzed by the test module reader 12. Further details of thedetection method are described later.

Additional Details for the LOC Device Modularity of the Design

The LOC device 301 has many functional sections, including the reagentreservoirs 54, 56, 58, 60 and 62, the dialysis section 70, lysis section130, incubation section 114, and amplification section 112, valve types,the humidifier and humidity sensor. In other embodiments of the LOCdevice, these functional sections can be omitted, additional functionalsections can be added or the functional sections can be used foralternative purposes to those described above.

For example, the incubation section 114 can be used as the firstamplification section 112 of a tandem amplification assay system, withthe chemical lysis reagent reservoir 56 being used to add the firstamplification mix of primers, dNTPs and buffer and reagent reservoir 58being used for adding the reverse transcriptase and/or polymerase. Achemical lysis reagent can also be added to the reservoir 56 along withthe amplification mix if chemical lysis of the sample is desired or,alternatively, thermal lysis can occur in the incubation section byheating the sample for a predetermined time. In some embodiments, anadditional reservoir can be incorporated immediately upstream ofreservoir 58 for the mix of primers, dNTPs and buffer if there is arequirement for chemical lysis and a separation of this mix from thechemical lysis reagent is desired.

In some circumstances it may be desirable to omit a step, such as theincubation step 291. In this case, a LOC device can be specificallyfabricated to omit the reagent reservoir 58 and incubation section 114,or the reservoir can simply not be loaded with reagents or the activevalves, if present, not activated to dispense the reagents into thesample flow, and the incubation section then simply becomes a channel totransport the sample from the lysis section 130 to the amplificationsection 112. The heaters are independently operable and therefore, wherereactions are dependent on heat, such as thermal lysis, programming theheaters not to activate during this step ensures thermal lysis does notoccur in LOC devices that do not require it. The dialysis section 70 canbe located at the beginning of the fluidic system within themicrofluidic device as shown in FIG. 4 or can be located anywhere elsewithin the microfluidic device. For example, dialysis after theamplification phase 292 to remove cellular debris prior to thehybridization and detection step 294 may be beneficial in somecircumstances. Alternatively, two or more dialysis sections can beincorporated at any location throughout the LOC device. Similarly, it ispossible to incorporate additional amplification sections 112 to enablemultiple targets to be amplified in parallel or in series prior to beingdetected in the hybridization chamber arrays 110 with specific nucleicacid probes. For analysis of samples like whole blood, in which dialysisis not required, the dialysis section 70 is simply omitted from thesample input and preparation section 288 of the LOC design. In somecases, it is not necessary to omit the dialysis section 70 from the LOCdevice even if the analysis does not require dialysis. If there is nogeometric hindrance to the assay by the existence of a dialysis section,a LOC with the dialysis section 70 in the sample input and preparationsection can still be used without a loss of the required functionality.

Furthermore, the detection section 294 may encompass proteomic chamberarrays which are identical to the hybridization chamber arrays but areloaded with probes designed to conjugate or hybridize with sample targetproteins present in non-amplified sample instead of nucleic acid probesdesigned to hybridize to target nucleic acid sequences.

It will be appreciated that the LOC devices fabricated for use in thisdiagnostic system are different combinations of functional sectionsselected in accordance with the particular LOC application. The vastmajority of functional sections are common to many of the LOC devicesand the design of additional LOC devices for new application is a matterof compiling an appropriate combination of functional sections from theextensive selection of functional sections used in the existing LOCdevices.

Only a small number of the LOC devices are shown in this description andsome more are shown schematically to illustrate the design flexibilityof the LOC devices fabricated for this system. The person skilled in theart will readily recognise that the LOC devices shown in thisdescription are not an exhaustive list and many additional LOC designsare a matter of compiling the appropriate combination of functionalsections.

Sample Types

LOC variants can accept and analyze the nucleic acid or protein contentof a variety of sample types in liquid form including, but not limitedto, blood and blood products, saliva, cerebrospinal fluid, urine, semen,amniotic fluid, umbilical cord blood, breast milk, sweat, pleuraleffusion, tear, pericardial fluid, peritoneal fluid, environmental watersamples and drink samples. Amplicon obtained from macroscopic nucleicacid amplification can also be analysed using the LOC device; in thiscase, all the reagent reservoirs will be empty or configured not torelease their contents, and the dialysis, lysis, incubation andamplification sections will be used solely to transport the sample fromthe sample inlet 68 to the hybridization chambers 180 for nucleic aciddetection, as described above.

For some sample types, a pre-processing step is required, for examplesemen may need to be liquefied and mucus may need to be pre-treated withan enzyme to reduce the viscosity prior to input into the LOC device.

Sample Input

Referring to FIGS. 1 and 12, the sample is added to the macroreceptacle24 of the test module 10. The macroreceptacle 24 is a truncated conewhich feeds into the inlet 68 of the LOC device 301 by capillary action.Here it flows into the 64 μm wide×60 μm deep cap channel 94 where it isdrawn towards the anticoagulant reservoir 54, also by capillary action.

reagent Reservoirs

The small volumes of reagents required by the assay systems usingmicrofluidic devices, such as LOC device 301, permit the reagentreservoirs to contain all reagents necessary for the biochemicalprocessing with each of the reagent reservoirs having a small volume.This volume is easily less than 1,000,000,000 cubic microns, in the vastmajority of cases less than 300,000,000 cubic microns, typically lessthan 70,000,000 cubic microns and in the case of the LOC device 301shown in the drawings, less than 20,000,000 cubic microns.

Dialysis Section

Referring to FIGS. 15 to 21, 33 and 34, the pathogen dialysis section 70is designed to concentrate pathogenic target cells from the sample. Aspreviously described, a plurality of apertures in the form of 3 microndiameter holes 164 in the roof layer 66 filter the target cells from thebulk of the sample. As the sample flows past the 3 micron diameterapertures 164, microbial pathogens pass through the holes into a seriesof dialysis MST channels 204 and flow back up into the target channel 74via 16 μm dialysis uptake holes 168 (see FIGS. 33 and 34). The remainderof the sample (erythrocytes and so on) stay in the cap channel 94.Downstream of the pathogen dialysis section 70, the cap channel 94becomes the waste channel 72 leading to the waste reservoir 76. Forbiological samples of the type that generate a substantial amount ofwaste, a foam insert or other porous element 49 within the outer casing13 of the test module 10 is configured to be in fluid communication withthe waste reservoir 76 (see FIG. 1).

The pathogen dialysis section 70 functions entirely on capillary actionof the fluid sample. The 3 micron diameter apertures 164 at the upstreamend of the pathogen dialysis section 70 have capillary initiationfeatures (CIFs) 166 (see FIG. 33) so that the fluid is drawn down intothe dialysis MST channel 204 beneath. The first uptake hole 198 for thetarget channel 74 also has a CIF 202 (see FIG. 15) to avoid the flowsimply pinning a meniscus across the dialysis uptake holes 168.

The small constituents dialysis section 682 schematically shown in FIG.71 can have a similar structure to the pathogen dialysis section 70. Thesmall constituents dialysis section separates any small target cells ormolecules from a sample by sizing (and, if necessary, shaping) aperturessuitable for allowing the small target cells or molecules to pass intothe target channel and continue for further analysis. Larger sized cellsor molecules are removed to a waste reservoir 766. Thus, the LOC device30 (see FIGS. 1 and 104) is not limited to separating pathogens that areless than 3 μm in size, but can be used to separate cells or moleculesof any size desired.

Lysis Section

Referring back to FIGS. 7, 11 and 13, the genetic material in the sampleis released from the cells by a chemical lysis process. As describedabove, a lysis reagent from the lysis reservoir 56 mixes with the sampleflow in the target channel 74 downstream of the surface tension valve128 for the lysis reservoir 56. However, some diagnostic assays arebetter suited to a thermal lysis process, or even a combination ofchemical and thermal lysis of the target cells. The LOC device 301accommodates this with the heated microchannels 210 of the incubationsection 114. The sample flow fills the incubation section 114 and stopsat the boiling-initiated valve 106. The incubation microchannels 210heat the sample to a temperature at which the cellular membranes aredisrupted.

In some thermal lysis applications, an enzymatic reaction in thechemical lysis section 130 is not necessary and the thermal lysiscompletely replaces the enzymatic reaction in the chemical lysis section130.

Boiling-Initiated Valve

As discussed above, the LOC device 301 has three boiling-initiatedvalves 126, 106 and 108. The location of these valves is shown in FIG.6. FIG. 31 is an enlarged plan view of the boiling-initiated valve 108in isolation at the end of the heated microchannels 158 of theamplification section 112.

The sample flow 119 is drawn along the heated microchannels 158 bycapillary action until it reaches the boiling-initiated valve 108. Theleading meniscus 120 of the sample flow pins at a meniscus anchor 98 atthe valve inlet 146. The geometry of the meniscus anchor 98 stops theadvancing meniscus to arrest the capillary flow. As shown in FIGS. 31and 32, the meniscus anchor 98 is an aperture provided by an uptakeopening from the MST channel 90 to the cap channel 94. Surface tensionin the meniscus 120 keeps the valve closed. An annular heater 152 is atthe periphery of the valve inlet 146. The annular heater 152 isCMOS-controlled via the boiling-initiated valve heater contacts 153.

To open the valve, the CMOS circuitry 86 sends an electrical pulse tothe valve heater contacts 153. The annular heater 152 resistively heatsuntil the liquid sample 119 boils. The boiling unpins the meniscus 120from the valve inlet 146 and initiates wetting of the cap channel 94.Once wetting the cap channel 94 begins, capillary flow resumes. Thefluid sample 119 fills the cap channel 94 and flows through the valvedowntake 150 to the valve outlet 148 where capillary driven flowcontinues along the amplification section exit channel 160 into thehybridization and detection section 52. Liquid sensors 174 are placedbefore and after the valve for diagnostics.

It will be appreciated that once the boiling-initiated valves areopened, they cannot be re-closed. However, as the LOC device 301 and thetest module 10 are single-use devices, re-closing the valves isunnecessary.

Incubation Section and Nucleic Acid Amplification Section

FIGS. 6, 7, 13, 14, 23, 24, 25, 35 to 45, 50 and 51 show the incubationsection 114 and the amplification section 112. The incubation section114 has a single, heated incubation microchannel 210 etched in aserpentine pattern in the MST channel layer 100 from the downtakeopening 134 to the boiling-initiated valve 106 (see FIGS. 13 and 14).Control over the temperature of the incubation section 114 enablesenzymatic reactions to take place with greater efficiency. Similarly,the amplification section 112 has a heated amplification microchannel158 in a serpentine configuration leading from the boiling-initiatedvalve 106 to the boiling-initiated valve 108 (see FIGS. 6 and 14). Thesevalves arrest the flow to retain the target cells in the heatedincubation or amplification microchannels 210 or 158 while mixing,incubation and nucleic acid amplification takes place. The serpentinepattern of the microchannels also facilitates (to some extent) mixing ofthe target cells with reagents.

In the incubation section 114 and the amplification section 112, thesample cells and the reagents are heated by the heaters 154 controlledby the CMOS circuitry 86 using pulse width modulation (PWM). Eachmeander of the serpentine configuration of the heated incubationmicrochannel 210 and amplification microchannel 158 has three separatelyoperable heaters 154 extending between their respective heater contacts156 (see FIG. 14) which provides for the two-dimensional control ofinput heat flux density. As best shown in FIG. 51, the heaters 154 aresupported on the roof layer 66 and embedded in the lower seal 64. Theheater material is TiAl but many other conductive metals would besuitable. The elongate heaters 154 are parallel with the longitudinalextent of each channel section that forms the wide meanders of theserpentine shape. In the amplification section 112, each of the widemeanders can operate as separate PCR chambers via individual heatercontrol.

The small volumes of amplicon required by the assay systems usingmicrofluidic devices, such as LOC device 301, permit low amplificationmixture volumes for amplification in amplification section 112. Thisvolume is easily less than 400 nanoliters, in the vast majority of casesless than 170 nanoliters, typically less than 70 nanoliters and in thecase of the LOC device 301, between 2 nanoliters and 30 nanoliters.

Increased Rates of Heating and Greater Diffusive Mixing

The small cross section of each channel section increases the heatingrate of the amplification fluid mix. All the fluid is kept a relativelyshort distance from the heater 154. Reducing the channel cross section(that is the amplification microchannel 158 cross section) to less than100,000 square microns achieves appreciably higher heating rates thanthat provided by more ‘macro-scale’ equipment. Lithographic fabricationtechniques allow the amplification microchannel 158 to have a crosssectional area transverse to the flow-path less than 16,000 squaremicrons which gives substantially higher heating rates. Feature sizes onthe order of 1 micron are readily achievable with lithographictechniques. If very little amplicon is needed (as is the case in the LOCdevice 301), the cross sectional area can be reduced to less than 2,500square microns. For diagnostic assays with 1,000 to 2,000 probes on theLOC device, and a requirement of ‘sample-in, answer out’ in less than 1minute, a cross sectional area transverse to the flow of between 400square microns and 1 square micron is adequate.

The heater element in the amplification microchannel 158 heats thenucleic acid sequences at a rate more than 80 Kelvin (K) per second, inthe vast majority of cases at a rate greater than 100 K per second.Typically, the heater element heats the nucleic acid sequences at a ratemore than 1,000 K per second and in many cases, the heater element heatsthe nucleic acid sequences at a rate more than 10,000 K per second.Commonly, based on the demands of the assay system, the heater elementheats the nucleic acid sequences at a rate more than 100,000 K persecond, more than 1,000,000 K per second more than 10,000,000 K persecond, more than 20,000,000 K per second, more than 40,000,000 K persecond, more than 80,000,000 K per second and more than 160,000,000 Kper second.

A small cross-sectional area channel is also beneficial for diffusivemixing of any reagents with the sample fluid. Before diffusive mixing iscomplete, diffusion of one liquid into the other is greatest near theinterface between the two. Concentration decreases with distance fromthe interface. Using microchannels with relatively small cross sectionstransverse to the flow direction, keeps both fluid flows close to theinterface for more rapid diffusive mixing. Reducing the channel crosssection to less than 100,000 square microns achieves appreciably highermixing rates than that provided by more ‘macro-scale’ equipment.Lithographic fabrication techniques allows microchannels with a crosssectional area transverse to the flow-path less than 16000 squaremicrons which gives significantly higher mixing rates. If small volumesare needed (as is the case in the LOC device 301), the cross sectionalarea can be reduced to less than 2500 square microns. For diagnosticassays with 1000 to 2000 probes on the LOC device, and a requirement of‘sample-in, answer out’ in less than 1 minute, a cross sectional areatransverse to the flow of between 400 square microns and 1 square micronis adequate.

Short Thermal Cycle Times

Keeping the sample mixture proximate to the heaters, and using verysmall fluid volumes allows rapid thermal cycling during the nucleic acidamplification process. Each thermal cycle (i.e. denaturing, annealingand primer extension) is completed in less than 30 seconds for targetsequences up to 150 base pairs (bp) long. In the vast majority ofdiagnostic assays, the individual thermal cycle times are less than 11seconds, and a large proportion are less than 4 seconds. LOC devices 30with some of the most common diagnostic assays have thermal cycles timebetween 0.45 seconds to 1.5 seconds for target sequences up to 150 bylong. Thermal cycling at this rate allows the test module to completethe nucleic acid amplification process in much less than 10 minutes;often less than 220 seconds. For most assays, the amplification sectiongenerates sufficient amplicon in less than 80 seconds from the samplefluid entering the sample inlet. For a great many assays, sufficientamplicon is generated in 30 seconds.

Upon completion of a preset number of amplification cycles, the ampliconis fed into the hybridization and detection section 52 via theboiling-initiated valve 108.

Hybridization Chambers

FIGS. 52, 53, 54, 56 and 57 show the hybridization chambers 180 in thehybridization chamber array 110. The hybridization and detection section52 has a 24×45 array 110 of hybridization chambers 180, each withhybridization-responsive FRET probes 186, heater element 182 and anintegrated photodiode 184. The photodiode 184 is incorporated fordetection of fluorescence resulting from the hybridization of a targetnucleic acid sequence or protein with the FRET probes 186. Eachphotodiode 184 is independently controlled by the CMOS circuitry 86. Anymaterial between the FRET probes 186 and the photodiode 184 must betransparent to the emitted light. Accordingly, the wall section 97between the probes 186 and the photodiode 184 is also opticallytransparent to the emitted light. In the LOC device 301, the wallsection 97 is a thin (approximately 0.5 micron) layer of silicondioxide.

Incorporation of a photodiode 184 directly beneath each hybridizationchamber 180 allows the volume of probe-target hybrids to be very smallwhile still generating a detectable fluorescence signal (see FIG. 54).The small amounts permit small volume hybridization chambers. Adetectable amount of probe-target hybrid requires a quantity of probe,prior to hybridization, which is easily less than 270 picograms(corresponding to 900,000 cubic microns), in the vast majority of casesless than 60 picograms (corresponding to 200,000 cubic microns),typically less than 12 picograms (corresponding to 40,000 cubic microns)and in the case of the LOC device 301 shown in the accompanying figures,less than 2.7 picograms (corresponding to a chamber volume of 9,000cubic microns). Of course, reducing the size of the hybridizationchambers allows a higher density of chambers and therefore more probeson the LOC device. In LOC device 301, the hybridization section has morethan 1,000 chambers in an area of 1,500 microns by 1,500 microns (i.e.less than 2,250 square microns per chamber). Smaller volumes also reducethe reaction times so that hybridization and detection is faster. Anadditional advantage of the small amount of probe required in eachchamber is that only very small quantities of probe solution need to bespotted into each chamber during production of the LOC device.Embodiments of the LOC device according to the invention can be spottedusing a probe solution volume of 1 picoliter or less.

After nucleic acid amplification, boiling-initiated valve 108 isactivated and the amplicon flows along the flow-path 176 and into eachof the hybridization chambers 180 (see FIGS. 52 and 56). An end-pointliquid sensor 178 indicates when the hybridization chambers 180 arefilled with amplicon and the heaters 182 can be activated.

After sufficient hybridization time, the LED 26 (see FIG. 2) isactivated. The opening in each of the hybridization chambers 180provides an optical window 136 for exposing the FRET probes 186 to theexcitation radiation (see FIGS. 52, 54 and 56). The LED 26 isilluminated for a sufficiently long time in order to induce afluorescence signal from the probes with high intensity. Duringexcitation, the photodiode 184 is shorted. After a pre-programmed delay300 (see FIG. 2), the photodiode 184 is enabled and fluorescenceemission is detected in the absence of the excitation light. Theincident light on the active area 185 of the photodiode 184 (see FIG.54) is converted into a photocurrent which can then be measured usingCMOS circuitry 86.

The hybridization chambers 180 are each loaded with probes for detectinga single target nucleic acid sequence. Each hybridization chambers 180can be loaded with probes to detect over 1,000 different targets ifdesired. Alternatively, many or all the hybridization chambers can beloaded with the same probes to detect the same target nucleic acidrepeatedly. Replicating the probes in this way throughout thehybridization chamber array 110 leads to increased confidence in theresults obtained and the results can be combined by the photodiodesadjacent those hybridization chambers to provide a single result ifdesired. The person skilled in the art will recognise that it ispossible to have from one to over 1,000 different probes on thehybridization chamber array 110, depending on the assay specification.

Hybridization Chambers with Electrochemiluminescence Detection

FIGS. 97, 120, 138 and 139 show the hybridization chambers 180 used inan ECL variant of the LOC device, LOC variant L 729. In this embodimentof the LOC device, a 24×45 array 110 of hybridization chambers 180, eachwith hybridization-responsive ECL probes 237, is positioned inregistration with a corresponding array of photodiodes 184 integratedinto the CMOS. In a similar fashion to the LOC devices configured forfluorescence detection, each photodiode 184 is incorporated fordetection of ECL resulting from the hybridization of a target nucleicacid sequence or protein with an ECL probe 237. Each photodiode 184 isindependently controlled by the CMOS circuitry 86. Again, thetransparent wall section 97 between the probes 186 and the photodiode184 is transparent to the emitted light.

A photodiode 184 closely adjacent each hybridization chamber 180 allowsthe amount of probe-target hybrids to be very small while stillgenerating a detectable ECL signal (see FIG. 97). The small amountspermit small volume hybridization chambers. A detectable amount ofprobe-target hybrid requires a quantity of probe, prior tohybridization, which is easily less than 270 picograms (corresponding toa chamber volume of 900,000 cubic microns), in the vast majority ofcases less than 60 picograms (corresponding to 200,000 cubic microns),typically less than 12 picograms (corresponding to 40,000 cubic microns)and in the case of the LOC device shown in the drawings less than 2.7picograms (corresponding to a chamber volume of 9,000 cubic microns). Ofcourse, reducing the size of the hybridization chambers allows a higherdensity of chambers and therefore more probes on the LOC device. In theLOC device shown, the hybridization section has more than 1,000 chambersin an area of 1,500 microns by 1,500 microns (i.e. less than 2,250square microns per chamber). Smaller volumes also reduce the reactiontimes so that hybridization and detection is faster. An additionaladvantage of the small amount of probe required in each chamber is thatonly very small quantities of probe solution need be spotted into eachchamber during production of the LOC device. In the case of the LOCdevice shown in the drawings, the required amount of probe can bespotted using a solution volume of 1 picoliter or less.

After nucleic acid amplification, the boiling-initiated valve 108 isactivated and the amplicon flows along the flow-path 176 and into eachof the hybridization chambers 180 (see FIGS. 52 and 139). An end-pointliquid sensor 178 indicates when the hybridization chambers 180 arefilled with amplicon so that the heaters 182 can be activated.

After sufficient hybridization time, the photodiode 184 is enabled readyfor collection of the ECL signal. Then the ECL excitation drivers 39(see FIG. 105) activate the ECL electrodes 860 and 870 for apredetermined length of time. The photodiode 184 remains active for ashort time after cessation of the ECL excitation current to maximize thesignal-to-noise ratio. For example, if the photodiode 184 remains activefor five times the decay lifetime of the luminescent emission, then thesignal will have decayed to less than one percent of the initial value.The incident light on the photodiode 184 is converted into aphotocurrent which can then be measured using CMOS circuitry 86.

Proteomic Assay Chambers

Some LOC variants, such as LOC variant L 729, are configured to performhomogeneous protein assays on crude cell lysates within proteomic assaychamber arrays (see for example 124.1 to 124.3 of FIGS. 116 and 120) forthe detection of host cell and/or pathogenic proteins. The proteomicassay chamber arrays 124.1-124.3 are manufactured and configured inexactly the same manner as the hybridization chamber arrays 110 (seeFIGS. 52, 53, 54 and 56). Each proteomic assay chamber has a diffusionbarrier 175 at the entrance to prevent diffusion of sample and reagentsbetween chambers, thus avoiding an erroneous result (see FIGS. 84 and85, which are insets DC and DD of FIG. 81). Where required for proteinhybridization or conjugation, thermal energy is provided byCMOS-controlled heaters 182 in each chamber. In some embodiments, anend-point liquid sensor 178 is used to indicate when the proteomic assaychambers are filled with sample so that the heaters 182 can beactivated. After sufficient time has elapsed, the fluorescent orelectrochemiluminescent signal generated following protein recognitionis detected by the photosensor 44.

Humidifier and Humidity Sensor

Inset AG of FIG. 6 indicates the position of the humidifier 196. Thehumidifier prevents evaporation of the reagents and probes duringoperation of the LOC device 301. As best shown in the enlarged view ofFIG. 55, a water reservoir 188 is fluidically connected to threeevaporators 190. The water reservoir 188 is filled with molecularbiology-grade water and sealed during manufacturing. As best shown inFIGS. 55 and 61, water is drawn into three downtakes 194 and alongrespective water supply channels 192 by capillary action to a set ofthree uptakes 193 at the evaporators 190. A meniscus pins at each uptake193 to retain the water. The evaporators have annular shaped heaters 191which encircle the uptakes 193. The annular heaters 191 are connected tothe CMOS circuitry 86 by the conductive columns 376 to the top metallayer 195 (see FIG. 37). Upon activation, the annular heaters 191 heatthe water causing evaporation and humidifying the device surrounds.

The position of the humidity sensor 232 is also shown in FIG. 6.However, as best shown in the enlarged view of Inset AH in FIG. 58, thehumidity sensor has a capacitive comb structure. A lithographicallyetched first electrode 296 and a lithographically etched secondelectrode 298 face each other such that their teeth are interleaved. Theopposed electrodes form a capacitor with a capacitance that can bemonitored by the CMOS circuitry 86. As the humidity increases, thepermittivity of the air gap between the electrodes increases, so thatthe capacitance also increases. The humidity sensor 232 is adjacent thehybridization chamber array 110 where humidity measurement is mostimportant to slow evaporation from the solution containing the exposedprobes.

Feedback Sensors

Temperature and liquid sensors are incorporated throughout the LOCdevice 301 to provide feedback and diagnostics during device operation.Referring to FIG. 35, nine temperature sensors 170 are distributedthroughout the amplification section 112 Likewise, the incubationsection 114 also has nine temperature sensors 170. These sensors eachuse a 2×2 array of bipolar junction transistors (BJTs) to monitor thefluid temperature and provide feedback to the CMOS circuitry 86. TheCMOS circuitry 86 uses this to precisely control the thermal cyclingduring the nucleic acid amplification process and any heating duringthermal lysis and incubation.

In the hybridization chambers 180, the CMOS circuitry 86 uses thehybridization heaters 182 as temperature sensors (see FIG. 56). Theelectrical resistance of the hybridization heaters 182 is temperaturedependent and the CMOS circuitry 86 uses this to derive a temperaturereading for each of the hybridization chambers 180.

The LOC device 301 also has a number of MST channel liquid sensors 174and cap channel liquid sensors 208. FIG. 35 shows a line of MST channelliquid sensors 174 at one end of every other meander in the heatedmicrochannel 158. As best shown in FIG. 37, the MST channel liquidsensors 174 are a pair of electrodes formed by exposed areas of the topmetal layer 195 in the CMOS structure 86. Liquid closes the circuitbetween the electrodes to indicate its presence at the sensor'slocation.

FIG. 25 shows an enlarged perspective of cap channel liquid sensors 208.Opposing pairs of TiAl electrodes 218 and 220 are deposited on the rooflayer 66. Between the electrodes 218 and 220 is a gap 222 to hold thecircuit open in the absence of liquid. The presence of liquid closes thecircuit and the CMOS circuitry 86 uses this feedback to monitor theflow.

Gravitational Independence

The test modules 10 are orientation independent. They do not need to besecured to a flat stable surface in order to operate. Capillary drivenfluid flows and a lack of external plumbing into ancillary equipmentallow the modules to be truly portable and simply plugged into asimilarly portable hand held reader such as a mobile telephone. Having agravitationally independent operation means the test modules are alsoaccelerationally independent to all practical extents. They areresistant to shock and vibration and will operate on moving vehicles orwhile the mobile telephone is being carried around.

Dialysis Variants Leukocyte Target

The dialysis design described above in the LOC device 301 targetspathogens. FIG. 59 is a schematic section view of a dialysis section 328designed to concentrate leukocytes from a blood sample for human DNAanalysis. It will be appreciated that the structure is essentially thesame as that of the pathogen target dialysis section 70 described abovewith the exception that apertures in the form of 7.5 micron diameterholes 165 restrict leukocytes from passing from the cap channel 94 tothe dialysis MST channels 204. In situations where the sample beinganalysed is a blood sample, and the presence of haemoglobin from theerythrocytes interferes with the subsequent reaction steps, addition ofan erythrocyte lysis buffer along with the anticoagulant in thereservoir 54 (see FIG. 22), will ensure that the majority of the lysederythrocytes (and hence haemoglobin) will be removed from the sampleduring this dialysis step. A commonly used erythrocyte lysis buffer is0.15M NH₄CL, 10 mM KHCO₃, 0.1 mM EDTA, pH 7.2-7.4, but a person skilledin the art will recognise that any buffer which efficiently lyseserythrocytes can be used.

Downstream of the leukocyte dialysis section 328, the cap channel 94becomes the target channel 74 such that the leukocytes continue as partof the assay. Furthermore, in this case, the dialysis uptake holes 168lead to a waste channel 72 so that all smaller cells and components inthe sample are removed. It should be noted that this dialysis variantonly reduces the concentration of the unwanted specimens in the targetchannel 74.

FIG. 72 schematically illustrates a large constituents dialysis section686 which also separates any large target constituents from a sample.The apertures in this dialysis section are fabricated with a size andshape tailored to withhold the large target constituents of interest inthe target channel for further analysis. As with the leukocyte dialysissection described above, most (but not all) smaller sized cells,organisms or molecules flow to a waste reservoir 768. Thus, otherembodiments of the LOC device are not limited to separating leukocytesthat are larger than 7.5 μm in size, but can be used to separate cells,organisms or molecules of any size desired.

Dialysis Section with Flow Channel to Prevent Trapped Air Bubbles

Described below is an embodiment of the LOC device referred to as LOCvariant VIII 518 and shown in FIGS. 65, 66, 67 and 68. This LOC devicehas a dialysis section that fills with the fluid sample without leavingair bubbles trapped in the channels. LOC variant VIII 518 also has anadditional layer of material referred to as an interface layer 594. Theinterface layer 594 is positioned between the cap channel layer 80 andthe MST channel layer 100 of the CMOS+MST device 48. The interface layer594 allows a more complex fluidic interconnection between the reagentreservoirs and the MST layer 87 without increasing the size of thesilicon substrate 84.

Referring to FIG. 66, the bypass channel 600 is designed to introduce atime delay in the fluid sample flow from the interface waste channel 604to the interface target channel 602. This time delay allows the fluidsample to flow through the dialysis MST channel 204 to the dialysisuptake 168 where it pins a meniscus. With a capillary initiation feature(CIF) 202 at the uptake from the bypass channel 600 to the interfacetarget channel 602, the sample fluid fills the interface target channel602 from a point upstream of all the dialysis uptakes 168 from thedialysis MST channels 204.

Without the bypass channel 600, the interface target channel 602 stillstarts filling from the upstream end, but eventually the advancingmeniscus reaches and passes over an uptake belonging to an MST channelthat has not yet filled, leading into air entrapment at that point.Trapped air reduces the sample flow rate through the leukocyte dialysissection 328.

Nucleic Acid Amplification Variants Direct PCR

Traditionally, PCR requires extensive purification of the target DNAprior to preparation of the reaction mixture. However, with appropriatechanges to the chemistry and sample concentration, it is possible toperform nucleic acid amplification with minimal DNA purification, ordirect amplification. When the nucleic acid amplification process isPCR, this approach is called direct PCR. In LOC devices where nucleicacid amplification is performed at a controlled, constant temperature,the approach is direct isothermal amplification. Direct nucleic acidamplification techniques have considerable advantages for use in LOCdevices, particularly relating to simplification of the required fluidicdesign. Adjustments to the amplification chemistry for direct PCR ordirect isothermal amplification include increased buffer strength, theuse of polymerases which have high activity and processivity, andadditives which chelate with potential polymerase inhibitors. Dilutionof inhibitors present in the sample is also important.

To take advantage of direct nucleic acid amplification techniques, theLOC device designs incorporate two additional features. The firstfeature is reagent reservoirs (for example reservoir 58 in FIG. 8) whichare appropriately dimensioned to supply a sufficient quantity ofamplification reaction mix, or diluent, so that the final concentrationsof sample components which might interfere with amplification chemistryare low enough to permit successful nucleic acid amplification. Thedesired dilution of non-cellular sample components is in the range of 5×to 20×. Different LOC structures, for example the pathogen dialysissection 70 in FIG. 4, are used when appropriate to ensure that theconcentration of target nucleic acid sequences is maintained at a highenough level for amplification and detection. In this embodiment,further illustrated in FIG. 6, a dialysis section which effectivelyconcentrates pathogens small enough to be passed into the amplificationsection 292 is employed upstream of the sample extraction section 290,and rejects larger cells to a waste receptacle 76. In anotherembodiment, a dialysis section is used to selectively deplete proteinsand salts in blood plasma while retaining cells of interest.

The second LOC structural feature which supports direct nucleic acidamplification is design of channel aspect ratios to adjust the mixingratio between the sample and the amplification mix components. Forexample, to ensure dilution of inhibitors associated with the sample inthe preferred 5×-20× range through a single mixing step, the length andcross-section of the sample and reagent channels are designed such thatthe sample channel, upstream of the location where mixing is initiated,constitutes a flow impedance 4×-19× higher than the flow impedance ofthe channels through which the reagent mixture flows. Control over flowimpedances in microchannels is readily achieved through control over thedesign geometry. The flow impedance of a microchannel increases linearlywith the channel length, for a constant cross-section. Importantly formixing designs, flow impedance in microchannels depends more strongly onthe smallest cross-sectional dimension. For example, the flow impedanceof a microchannel with rectangular cross-section is inverselyproportional to the cube of the smallest perpendicular dimension, whenthe aspect ratio is far from unity.

Reverse-Transcriptase PCR (RT-PCR)

Where the sample nucleic acid species being analysed or extracted isRNA, such as from RNA viruses or messenger RNA, it is first necessary toreverse transcribe the RNA into complementary DNA (cDNA) prior to PCRamplification. The reverse transcription reaction can be performed inthe same chamber as the PCR (one-step RT-PCR) or it can be performed asa separate, initial reaction (two-step RT-PCR). In the LOC variantsdescribed herein, a one-step RT-PCR can be performed simply by addingthe reverse transcriptase to reagent reservoir 62 along with thepolymerase and programming the heaters 154 to cycle firstly for thereverse transcription step and then progress onto the nucleic acidamplification step. A two-step RT-PCR could also be easily achieved byutilizing the reagent reservoir 58 to store and dispense the buffers,primers, dNTPs and reverse transcriptase and the incubation section 114for the reverse transcription step followed by amplification in thenormal way in the amplification section 112.

Isothermal Nucleic Acid Amplification

For some applications, isothermal nucleic acid amplification is thepreferred method of nucleic acid amplification, thus avoiding the needto repetitively cycle the reaction components through varioustemperature cycles but instead maintaining the amplification section ata constant temperature, typically around 37° C. to 41° C. A number ofisothermal nucleic acid amplification methods have been described,including Strand Displacement Amplification (SDA), TranscriptionMediated Amplification (TMA), Nucleic Acid Sequence Based Amplification(NASBA), Recombinase Polymerase Amplification (RPA), Helicase-Dependentisothermal DNA Amplification (HDA), Rolling Circle Amplification (RCA),Ramification Amplification (RAM) and Loop-mediated IsothermalAmplification (LAMP), and any of these, or other isothermalamplification methods, can be employed in particular embodiments of theLOC device described herein.

In order to perform isothermal nucleic acid amplification, the reagentreservoirs 60 and 62 adjoining the amplification section will be loadedwith the appropriate reagents for the specified isothermal methodinstead of PCR amplification mix and polymerase. For example, for SDA,reagent reservoir 60 contains amplification buffer, primers and dNTPsand reagent reservoir 62 contains an appropriate nickase enzyme andExo-DNA polymerase. For RPA, reagent reservoir 60 contains theamplification buffer, primers, dNTPs and recombinase proteins, withreagent reservoir 62 containing a strand displacing DNA polymerase suchas Bsu. Similarly, for HDA, reagent reservoir 60 contains amplificationbuffer, primers and dNTPs and reagent reservoir 62 contains anappropriate DNA polymerase and a helicase enzyme to unwind the doublestranded DNA strand instead of using heat. The skilled person willappreciate that the necessary reagents can be split between the tworeagent reservoirs in any manner appropriate for the nucleic acidamplification process.

For amplification of viral nucleic acids from RNA viruses such as HIV orhepatitis C virus, NASBA or TMA is appropriate as it is unnecessary tofirst transcribe the RNA to cDNA. In this example, reagent reservoir 60is filled with amplification buffer, primers and dNTPs and reagentreservoir 62 is filled with RNA polymerase, reverse transcriptase and,optionally, RNase H.

For some forms of isothermal nucleic acid amplification it may benecessary to have an initial denaturation cycle to separate the doublestranded DNA template, prior to maintaining the temperature for theisothermal nucleic acid amplification to proceed. This is readilyachievable in all embodiments of the LOC device described herein, as thetemperature of the mix in the amplification section 112 can be carefullycontrolled by the heaters 154 in the amplification microchannels 158(see FIG. 14).

Isothermal nucleic acid amplification is more tolerant of potentialinhibitors in the sample and, as such, is generally suitable for usewhere direct nucleic acid amplification from the sample is desired.Therefore, isothermal nucleic acid amplification is sometimes useful inLOC variant XLIII 673, LOC variant XLIV 674 and LOC variant XLVII 677,amongst others, shown in FIGS. 73, 74 and 75, respectively. Directisothermal amplification may also be combined with one or morepre-amplification dialysis steps 70, 686 or 682 as shown in FIGS. 73 and75 and/or a pre-hybridization dialysis step 682 as indicated in FIG. 74to help partially concentrate the target cells in the sample beforenucleic acid amplification or remove unwanted cellular debris prior tothe sample entering the hybridization chamber array 110, respectively.The person skilled in the art will appreciate that any combination ofpre-amplification dialysis and pre-hybridization dialysis can be used.

Isothermal nucleic acid amplification can also be performed in parallelamplification sections such as those schematically represented in FIGS.64, 69 and 70, multiplexed and some methods of isothermal nucleic acidamplification, such as LAMP, are compatible with an initial reversetranscription step to amplify RNA.

Other Design Variants Flow Rate Sensor

In addition to temperature and liquid sensors, the LOC device can alsoincorporate CMOS-controlled flow rate sensors 740, as schematicallyillustrated in FIG. 94 and in LOC Variant X 728 (see FIGS. 76 to 92).The sensors are used to determine the flow rate in two steps. In thefirst step, the temperature of the serpentine heater element 814 isdetermined by applying a low current and measuring the voltage todetermine the resistance of the serpentine heater element 814, andtherefore the temperature of the element 814 using the knownrelationship between resistance and the temperature of the heaterelement. At this stage, minimal heat is being dissipated in the element814 and the temperature of the liquid in the channel is equal to thecalculated temperature of the element 814. In the second step, a highercurrent is applied to the serpentine heater element 814 such that thetemperature of the element 814 increases and some heat is lost to theflowing liquid. By again measuring the voltage across the element 814while the higher current is being applied, the new resistance of theelement 814 is determined and the increased temperature is againcalculated by the CMOS circuitry 86. Using the new temperature of theserpentine heater element 814 and the known temperature of sample liquidcalculated in the first step, the flow speed of the liquid isdetermined. From the known channel cross sectional geometry and the flowspeed, the flow rate of the liquid in the channel is calculated.

Protein Detection Variants

Some embodiments of the LOC device use a homogeneous protein detectionassay to detect specific proteins within a crude cell lysate. Numeroushomogeneous protein detection assays have been developed for use inthese embodiments of the LOC device. Commonly, these assays utilizeantibodies or aptamers to capture the target protein.

In one type of assay, an aptamer 141 which binds to a particular protein142 is labelled with two different fluorophores or luminophores 143 and144 which can function as a donor and an acceptor in a fluorescenceresonance energy transfer (FRET) or electrochemiluminescence resonanceenergy transfer (ERET) reaction (see FIGS. 108A and 108B ). Both donor143 and acceptor 144 are linked to the same aptamer 141, and the changein separation is caused by a change in conformation upon binding to thetarget protein 142. For example, an aptamer 141 in the absence of thetarget forms a conformation where the donor and acceptor are in closeproximity (see FIG. 108A); upon binding to the target, the newconformation results in a larger separation between the donor andacceptor (see FIG. 108B). When the acceptor is a quencher and the donoris a luminophore, the effect of binding to the target is an increase inlight emission 250 or 862 (see FIG. 108B).

A second type of assay uses two antibodies 145 or two aptamers 141 thatmust independently bind to different, non-overlapping epitopes orregions of the target protein 142 (see FIGS. 109A, 109B, 110A and 110B).These antibodies 145 or aptamers 141 are labelled with differentfluorophores or luminophores 143 and 144 which can function as a donorand an acceptor in a fluorescence resonance energy transfer (FRET) orelectrochemiluminescence resonance energy transfer (ERET) reaction. Thefluorophores or luminophores 143 and 144 form part of a pair of shortcomplementary oligonucleotides 147 attached to the antibodies oraptamers via long, flexible linkers 149 (see FIGS. 109A and 110A). Oncethe antibodies 145 or aptamers 141 bind to the target protein 142, thecomplementary oligonucleotides 147 find each other and hybridize to oneanother (see FIGS. 109B and 110B). This brings the donors and acceptors143 and 144 in close proximity to one another resulting in efficientFRET 250 or ERET 862 that is used as a signal for target proteindetection.

To ensure there is no, or very little, background signal as a result ofthe oligonucleotides 147 attached to the two antibodies 145 or aptamers141 hybridizing to one another in the absence of their binding to theprotein 142, it is necessary to carefully choose the length and sequenceof the complementary oligonucleotides 147 so that the dissociationconstant (k_(d)) for the duplex is relatively high (˜5 μM). Thus whenfree antibodies or aptamers labelled with these oligonucleotides aremixed at nanomolar concentrations, well below that of their k_(d), thelikelihood of duplex formation and a FRET 250 or ERET 862 signal beinggenerated is negligible. However, when both antibodies 145 or bothaptamers 141 bind to the target protein 142, the local concentration ofthe oligonucleotides 147 will be much higher than their k_(d) resultingin almost complete hybridization and generation of a detectable FRET 250or ERET 862 signal.

The choice of fluorophores and luminophores is an importantconsideration when designing a homogeneous protein detection assay.Crude cell lysates are often turbid and may contain substances whichautofluoresce. In such cases, the use of molecules with long-lastingfluorescence or electrochemiluminescence and donor-acceptor pairs 143and 144 which are optimized to give maximal FRET 250 or ERET 862 isdesired. One such pair is europium chelate and Cy5, which has previouslybeen shown to significantly improve signal-to-background ratio in such asystem when compared with other donor-acceptor pairs, by allowing thesignal to be read after interfering background fluorescence,electrochemiluminescence or scattered light has decayed. Europiumchelate and AlexaFluor 647 or terbium chelate and Fluorescein FRET orERET pairs also work well. The sensitivity and specificity of thisapproach is similar to that of enzyme-linked immunosorbent assays(ELISAs), but no sample manipulation is required.

In some embodiments of the LOC device, one of the antibodies 145 or oneof the aptamers 141 is attached to the base of the proteomic assaychamber 124 (see for example FIGS. 116 and 120) and the protein lysateis combined with the other antibody 145 or aptamer 141 during lysiswithin the chemical lysis section 130 to facilitate binding to the firstantibody 145 or aptamer 141 prior to entering the proteomic assaychamber 124. This increases the subsequent speed with which a detectablesignal is generated as only one conjugation or hybridization event isrequired within the proteomic assay chamber.

Photodiode

FIG. 54 shows the photodiode 184 integrated into the CMOS circuitry 86of the LOC device 301. The photodiode 184 is fabricated as part of theCMOS circuitry 86 without additional masks or steps. This is onesignificant advantage of a CMOS photodiode over a CCD, an alternatesensing technology which could be integrated on the same chip usingnon-standard processing steps, or fabricated on an adjacent chip.On-chip detection is low cost and reduces the size of the assay system.The shorter optical path length reduces noise from the surroundingenvironment for efficient collection of the fluorescence signal andeliminates the need for a conventional optical assembly of lenses andfilters.

Quantum efficiency of the photodiode 184 is the fraction of photonsimpinging on its active area 185 that are effectively converted tophoto-electrons. For standard silicon processes, the quantum efficiencyis in the range of 0.3 to 0.5 for visible light, depending on processparameters such as the amount and absorption properties of the coverlayers.

The detection threshold of the photodiode 184 determines the smallestintensity of the fluorescence signal that can be detected. The detectionthreshold also determines the size of the photodiode 184 and hence thenumber of hybridization chambers 180 in the hybridization and detectionsection 52 (see FIG. 52). The size and number of chambers are technicalparameters that are limited by the dimensions of the LOC device (in thecase of the LOC device 301, the dimensions are 1760 μm×5824 μm) and thereal estate available after other functional modules such as thepathogen dialysis section 70 and amplification section(s) 112 areincorporated.

For standard silicon processes, the photodiode 184 detects a minimum of5 photons. However, to ensure reliable detection, the minimum can be setto 10 photons. Therefore with the quantum efficiency range being 0.3 to0.5 (as discussed above), the fluorescence emission from the probesshould be a minimum of 17 photons but 30 photons would incorporate asuitable margin of error for reliable detection.

Electrochemiluminescence as an Alternative Detection Method

Electrochemiluminescence (ECL) involves the generation of species atelectrode surfaces that then undergo electron-transfer reactions to formexcited states that emit light. Electrochemiluminescence differs fromnormal chemiluminescence in that formation of the excited species relieson oxidation or reduction of the luminophore or a coreactant at anelectrode. Coreactants, in this context, are additional reagents addedto the ECL solution which enhance the efficiency of ECL emission. Innormal chemiluminescence, the excited species form purely through mixingof suitable reagents. The emitting atom or complex is traditionallyreferred to as a luminophore. In brief, ECL relies on generating anexcited state of the luminophore, at which point a photon will beemitted. As with any such process, it is possible for an alternate pathto be taken from the excited state which does not lead to the desiredlight emission (i.e. quenching).

Embodiments of the test module that use ECL instead of fluorescencedetection do not require an excitation LED. Electrodes are fabricatedwithin the hybridization chambers to provide the electrical pulse forECL generation and the photons are detected using the photosensor 44.The duration and voltage of the electrical pulse are controlled; in someembodiments, control over the current is used as an alternative tocontrolling the voltage.

Luminophore and Quencher

The ruthenium complex, [Ru(bpy)₃]²⁺, described previously for use as afluorescent reporter in the probes, can also be used as a luminophore inan ECL reaction in the hybridization chambers, with TPrA(tri-n-propylamine (CH₃CH₂—CH₂)₃N) as the coreactant. Coreactant ECL hasthe benefit that luminophores are not consumed after photon emission andthe reagents are available for the process to repeat. Furthermore, the[Ru(bpy)₃]²⁺/TPrA ECL system provides good signal levels atphysiologically relevant conditions of pH in aqueous solutions.Alternative coreactants which can produce equivalent or better resultsthan TPrA with ruthenium complexes are N-butyldiethanolamine and2-(dibutylamino)ethanol.

FIG. 95 illustrates the reactions occurring during an ECL process inwhich [Ru(bpy)₃]²⁺ is the luminophore 864 and TPrA is the coreactant866. ECL emission 862 in the [Ru(bpy)₃]²⁺/TPrA ECL system follows theoxidation of both Ru(bpy)₃ ²⁺ and TPrA at the anode 860. The reactionsare as follows:

Ru(bpy)₃ ²⁺−⁻→Ru(bpy)₃ ³⁺  (1)

TPrA−e⁻→[TPrA^(•)]⁺→TPrA^(•)+H⁺  (2)

Ru(bpy)₃ ³⁺+TPrA^(•)→Ru(bpy)₃ ^(•2+)+products   (3)

Ru(bpy)₃ ^(•2+)→Ru(bpy)₃ ²⁺+hυ  (4)

The wavelength of the emitted light 862 is around 620 nm and the anodepotential is around 1.1 V with respect to a Ag/AgCl reference electrode.For the [Ru(bpy)₃]²⁺/TPrA ECL system, either the Black Hole Quencher,BHQ 2, or Iowa Black RQ described previously, would be a suitablequencher. In the embodiments described here, the quencher is afunctional moiety which is initially attached to the probe, but otherembodiments are possible in which the quencher is a separate moleculefree in solution.

Hybridization Probes for ECL Detection

FIGS. 129 and 130 show the hybridization-responsive ECL probes 237.These are often referred to as molecular beacons and are stem-and-loopprobes, generated from a single strand of nucleic acid, that luminesceupon hybridization to complementary nucleic acids. FIG. 129 shows asingle ECL probe 237 prior to hybridization with a target nucleic acidsequence 238. The probe has a loop 240, stem 242, a luminophore 864 atthe 5′ end, and a quencher 248 at the 3′ end. The loop 240 consists of asequence complementary to the target nucleic acid sequence 238.Complementary sequences on either side of the probe sequence annealtogether to form the stem 242.

In the absence of a complementary target sequence, the probe remainsclosed as shown in FIG. 129. The stem 242 keeps the luminophore-quencherpair in close proximity to each other, such that significant resonantenergy transfer can occur between them, substantially eliminating theability of the luminophore to emit light after electrochemicalexcitation.

FIG. 130 shows the ECL probe 237 in an open or hybridized configuration.Upon hybridization to a complementary target nucleic acid sequence 238,the stem-and-loop structure is disrupted, the luminophore 864 andquencher 248 are spatially separated, thus restoring the ability of theluminophore 864 to emit light. The ECL emission 862 is opticallydetected as an indication that the probe has hybridized.

The probes hybridize with very high specificity with complementarytargets, since the stem helix of the probe is designed to be more stablethan a probe-target helix with a single nucleotide that is notcomplementary. Since double-stranded DNA is relatively rigid, it issterically impossible for the probe-target helix and the stem helix tocoexist.

Primer-Linked ECL Probes

Primer-linked stem-and-loop probes and primer-linked linear probes,otherwise known as scorpion probes, are an alternative to molecularbeacons and can be used for real-time and quantitative nucleic acidamplification in the LOC device. Real-time amplification is performeddirectly in the hybridization chambers of the LOC device. The benefit ofusing primer-linked probes is that the probe element is physicallylinked to the primer, thus only requiring a single hybridization eventto occur during the nucleic acid amplification rather than separatehybridizations of the primers and probes being required. This ensuresthat the reaction is effectively instantaneous and results in strongersignals, shorter reaction times and better discrimination than whenusing separate primers and probes. The probes (along with polymerase andthe amplification mix) would be deposited into the hybridizationchambers 180 during fabrication and there would be no need for anamplification section on the LOC device. Alternatively, theamplification section is left unused or used for other reactions.

Primer-Linked Linear ECL Probes

FIGS. 131 and 132 show a primer-linked linear ECL probe 693 during theinitial round of nucleic acid amplification and in its hybridizedconfiguration during subsequent rounds of nucleic acid amplification,respectively. Referring to FIG. 131, the primer-linked linear ECL probe693 has a double-stranded stem segment 242. One of the strandsincorporates the primer linked probe sequence 696 which is homologous toa region on the target nucleic acid 696 and is labelled on its 5′ endwith luminophore 864, and linked on its 3′ end to an oligonucleotideprimer 700 via an amplification blocker 694. The other strand of thestem 242 is labelled at its 3 end with a quencher molecule 248. Afterthe initial round of nucleic acid amplification has completed, the probecan loop around and hybridize to the extended strand with the, now,complementary sequence 698. During the initial round of nucleic acidamplification, the oligonucleotide primer 700 anneals to the target DNA238 (see FIG. 131) and is then extended, forming a DNA strand containingboth the probe sequence and the amplification product. The amplificationblocker 694 prevents the polymerase from reading through and copying theprobe region 696. Upon subsequent denaturation, the extendedoligonucleotide primer 700/template hybrid is dissociated and so is thedouble stranded stem 242 of the primer-linked linear probe, thusreleasing the quencher 248. Once the temperature decreases for theannealing and extension steps, the primer linked probe sequence 696 ofthe primer-linked linear ECL probe curls around and hybridizes to theamplified complementary sequence 698 on the extended strand and lightemission is detected indicating the presence of the target DNA.Non-extended primer-linked linear ECL probes retain theirdouble-stranded stem and light emission remains quenched. This detectionmethod is particularly well suited for fast detection systems as itrelies on a single-molecule process.

Primer-Linked Stem-and-Loop ECL Probes

FIGS. 133A to 133F show the operation of a primer-linked stem-and-loopECL probe 705. Referring to FIG. 133A, the primer-linked stem-and-loopECL probe 705 has a stem 242 of complementary double-stranded DNA and aloop 240 which incorporates the probe sequence. One of the stem strands708 is labelled at its 5′ end with luminophore 864. The other strand 710is labelled with a 3′-end quencher 248 and carries both theamplification blocker 694 and oligonucleotide primer 700. During theinitial denaturation phase (see FIG. 133B), the strands of the targetnucleic acid 238 separate, as does the stem 242 of the primer-linkedstem-and-loop ECL probe 705. When the temperature cools for theannealing phase (see FIG. 133C), the oligonucleotide primer 700 on theprimer-linked stem-and-loop ECL probe 705 hybridizes to the targetnucleic acid sequence 238. During extension (see FIG. 133D), thecomplement 706 to the target nucleic acid sequence 238 is synthesizedforming a DNA strand containing both the probe sequence 705 and theamplified product. The amplification blocker 694 prevents the polymerasefrom reading through and copying the probe region 705. When the probenext anneals, following denaturation (see FIG. 133E), the probe sequenceof the loop segment 240 of the primer-linked stem-and-loop probe (seeFIG. 133F) anneals to the complementary sequence 706 on the extendedstrand. This configuration leaves the luminophore 864 relatively remotefrom the quencher 248, resulting in a significant increase in lightemission.

ECL Control Probes

The hybridization chamber array 110 includes some hybridization chambers180 with positive and negative ECL control probes used for assay qualitycontrol. FIGS. 134 and 135 schematically illustrate negative control ECLprobes 786 without a luminophore, and FIGS. 136 and 137 are sketches ofpositive control ECL probes 787 without a quencher. The positive andnegative control ECL probes have a stem-and-loop structure like the ECLprobes described above. However, an ECL signal 862 (see FIG. 130) willalways be emitted from positive control ECL probes 787 and no ECL signal862 is ever emitted from negative control ECL probes 786, regardless ofwhether the probes hybridize into an open configuration or remainclosed.

Referring to FIGS. 134 and 135, the negative control ECL probe 786 hasno luminophore (and may or may not have a quencher 248). Hence, whetherthe target nucleic acid sequence 238 hybridizes with the probe as shownin FIG. 135, or the probe remains in its stem 242 and loop 240configuration as shown in FIG. 134, the ECL signal is negligible.Alternatively, the negative control ECL probe could be designed so thatit always remains quenched. For example, by having an artificial probe(loop) sequence 240 that will not hybridize to any nucleic acid sequencewithin the sample under investigation, the stem 242 of the probemolecule will re-hybridize to itself and the luminophore and quencherwill remain in close proximity and no appreciable ECL signal will bedetected. This negative control would account for any low level emissionthat may occur if the quenching is not complete.

Conversely, the positive control ECL probe 787 is constructed without aquencher as illustrated in FIGS. 136 and 137. Nothing quenches the ECLemission 862 from the luminophore 864 regardless of whether the positivecontrol probe 787 hybridizes with the target nucleic acid sequence 238.

FIGS. 123 and 124 show another possibility for constructing a positivecontrol chamber. In this case, the calibration chambers 382 which aresealed from the amplicon (or any flow containing target molecules) canbe filled with the ECL luminophore solution such that a positive signalis always detected at the electrode

Similarly, the control chambers can be negative control chambers becausethe lack of inlets prevents any targets from reaching the probes suchthat an ECL signal is never detected.

FIG. 52 shows a possible distribution of the positive and negativecontrol probes (378 and 380 respectively) throughout the hybridizationchamber array 110. For ECL, positive and negative control ECL probes 786and 787 would replace control fluorescent probes 378 and 380,respectively. The control probes are placed in hybridization chambers180 along a line extending diagonally across the hybridization chamberarray 110. However, the arrangement of the control probes within thearray is arbitrary (as is the configuration of the hybridization chamberarray 110).

Calibration Chambers for ECL Detection

The non-uniformity of the electrical characteristic of the photodiode184, response to any ambient light present at the sensor array, andlight originating at other locations in the array, introduce backgroundnoise and offset into the output signal. This background is removed fromeach output signal by calibration chambers 382 in the hybridizationchamber array 110 which either do not contain any probes, contain probesthat have no ECL luminophore, or contain probes with a luminophore andquencher configured such that quenching is always expected to occur. Thenumber and arrangement of the calibration chambers 382 throughout thehybridization chamber array is arbitrary. However, the calibration ismore accurate if photodiodes 184 are calibrated by a calibration chamber382 that is relatively proximate. Referring to FIG. 139, thehybridization chamber array 110 has one calibration chamber 382 forevery eight hybridization chambers 180. That is, a calibration chamber382 is positioned in the middle of every three by three square ofhybridization chambers 180. In this configuration, the hybridizationchambers 180 are calibrated by a calibration chamber 382 that isimmediately adjacent.

FIG. 93 shows a differential imager circuit 788 used to substract thesignal from the photodiode 184 corresponding to the calibration chamber382 as a result of the applied electrical pulse, from the ECL signalfrom the surrounding hybridization chambers 180. The differential imagercircuit 788 samples the signal from the pixel 790 and a “dummy” pixel792. Signals arising from ambient light in the region of the chamberarray are also subtracted. The signals from the pixel 790 are small(i.e. close to dark signal), and without a reference to a dark level itis hard to differentiate between the background and a very small signal.

During use, the “read_row” 794 and “read_row_d” 795 are activated and M4797 MD4 801 transistors are turned on. Switches 807 and 809 are closedsuch that the outputs from the pixel 790 and “dummy” pixel 792 arestored on pixel capacitor 803 and dummy pixel capacitor 805respectively. After the pixel signals have been stored, switches 807 and809 are deactivated. Then the “read_col” switch 811 and dummy “read_col”switch 813 are closed, and the switched capacitor amplifier 815 at theoutput amplifies the differential signal 817.

ECL Levels and Signal Efficiency

The normal metric of efficiency in ECL is the number of photons obtainedper “Faradaic” electron, i.e. per electron which participates in theelectrochemistry. The ECL efficiency is denoted φ_(ECL):

$\begin{matrix}{\varphi_{ECL} = \frac{\int_{0}^{t}{I{\tau}}}{\left( \frac{N_{A}}{F} \right){\int_{0}^{t}{{\tau}}}}} & (5)\end{matrix}$

where I is the intensity in photons per second, i is the current inamperes, F is Faraday's constant, and N_(A) is Avogadro's constant.

Efficiency of Coreacctant ECL

Annihilation ECL in deoxygenated, aprotic solutions (e.g.nitrogen-flushed acetonitrile solutions) is simple enough to allowefficiency measurements, and the consensus value of φ_(ECL) is around5%. Coreactant systems, however, have been generally declared to bebeyond meaningful direct measurements of efficiency. Instead, emissionintensity is related by scaling to easily-prepared standard solutionssuch as Ru(bpy)₃ ²⁺, measured in the same format. The literature (seefor example J. K. Leland and M. J. Powell, J. Electrochem. Soc., 137,3127 (1990), and R. Pyati and M. M. Richter, Annu. Rep. Prog. Chem. C,103, 12-78 (2007)) indicates that (without enhancers such assurfactants), the efficiency of Ru(bpy)₃ ²⁺ ECL with TPrA coreactantspeaks at levels comparable to the 5% seen for annihilation ECL inacetonitrile (e.g. 2% efficiency; see I. Rubinstein & A. J. Bard, J. Am.Chem. Soc., 103 512-516 (1981)).

ECL Potentials

The voltage at the working electrode for the Ru(bpy)₃ ²⁺/TPrA system isapproximately +1.1 V (generally measured in the literature with respectto a reference Ag/AgCl electrode). Voltages this high shorten electrodelifetimes but this is not an issue for single-use devices such as theLOC device used in the present diagnostic system.

The ideal voltage between the anode and cathode depends on thecombination of solution components and electrode materials. Selectingthe correct voltage can require compromising between the highest signallevels, reagent and electrode stability, and the activation of undesiredside reactions such as electrolysis of the water in the chamber. Intests on buffered aqueous Ru(bpy)₃₁ ²⁺/coreactant solution and platinumelectrodes, the ECL emission is maximized at 2.1-2.2 V (depending on thecoreactant choice). Emission intensities drop to <75% of the peak valuesfor voltages below 1.9 V and above 2.6 V, and to <50% of the peak valuesfor voltages below 1.7 V and above 2.8 V. A preferred anode-cathodevoltage difference for ECL operation in such systems is therefore1.7-2.8 V, with the range 1.9-2.6 V being particularly preferred. Thisallows maximization of the emission intensity as a function of voltage,while avoiding voltages at which significant gas evolution at theelectrodes is observed.

ECL Emission Wavelength

The wavelength of the emitted light 862 from ECL has an intensity peakat around 620 nm (measured in air or vacuum), and the emission spans arelatively broad wavelength range. Significant emission occurs atwavelengths from around 550 nm to 700 nm. Furthermore, the peak emissionwavelength can vary by ˜10% due to changes in the chemical environmentaround the active species. The LOC device embodiments described here,which incorporate no wavelength-specific filters, have two advantagesfor capturing signals with such a broad and variable spectrum. The firstadvantage is sensitivity: any wavelength filter reduces lighttransmission, even within its pass band, so efficiency is improved bynot including a filter. The second advantage is flexibility: adjustmentof filter pass bands is not required after minor reagent changes, andthe signals are less dependent on minor differences in non-targetcomponents of the input sample.

Solution Volume Participating in ECL

ECL relies on the availability of luminophore (and coreactant) insolution. However, as illustrated in FIG. 97, the excited species 868are generated only in the solution 872 near the electrodes 860 and 870.The parameter boundary layer depth in the models presented here, is thedepth of the layer of solution 872 around the electrode 860 in which theexcited species 868 are generated.

This is a simplification, since solution dynamics can drive theavailable concentration upward or downward:

-   -   Increased availability: diffusion and electrophoretic effects        will allow exchange with more of the solution.    -   Decreased availability: reagents can adsorb onto the electrodes        and may become unavailable to the ECL process.

For a boundary layer depth value of 0.5 μm, the following observationsare made:

ECL is observed in experiments where conjugation to magnetic beads withdiameters up to 4.5 μm is used to attract the luminophore 864 to theanode 860.

Ru(bpy)₃ ²⁺/TPrA ECL emission 862 as a function of electrode spacing,for interdigitated electrode arrays, was found to be maximised at a 0.8μm electrode spacing. The requirement for a coreactant 866 in aqueoussolutions 872 can be lifted when electrode spacings are ˜2 μm. Thisindicates that the excited species 868 diffuse multiple microns, whichimplies diffusive exchange on a similar scale for the species in theground state.

Steady State and Pulsed Operation

During pulsed activation of the electrodes 860 and 870, the intensity ofthe ECL emission 862 (see FIG. 130) is generally higher than theintensity of the emission 862 from steady-state activation of theelectrodes. Accordingly, the activation signal to the electrodes 860 and870 is pulse-width modulated (PWM) by the CMOS circuitry 86 (see FIG.102).

Reagent Recycling and Species Lifetime

The Ru complex is not consumed in the Ru(bpy)₃ ²⁺/TPrA ECL system, sothe intensity of emission 862 does not reduce with successive reactioncycles. The lifetime of the rate-limiting step is approximately 0.2milliseconds giving a total reaction recycling time of approximately 1millisecond.

Electrophoretic Effects and Other Constraints

Given the complexity of the solutions in the hybridization chamber, alarge number of phenomena take place when the ECL voltage is turned on.Electrophoresis of macromolecules, ohmic conduction, and capacitiveeffects from small ion migration occur simultaneously.

Electrophoresis of the oligonucleotides (probes and amplicon) cancomplicate the detection of probe-target hybrids, as DNA is highlynegatively charged and attracted to the anode 860. The time scale forthis motion is typically short (in the order of milliseconds).Electrophoretic effects are strong even though the voltages are moderate(˜1 V), because the separation between the anode 860 and cathode 870 issmall.

Electrophoresis enhances the ECL emission 862 in some embodiments of theLOC device and degrades the emission in others. This is addressed byincreasing or decreasing the electrode spacing to get the associatedincreases or decreases in electrophoretic effect. Interdigitation of theanode 860 and the cathode 870 above the photodiode 184 represents theextreme case of minimizing this separation. Such an arrangement producesECL, even in the absence of a coreactant 866 at carbon electrodes 860and 870.

Ohmic Heating (DC Current)

The current required to maintain an ECL voltage of ˜2.2 V, is determinedas follows with reference to the ECL cell 874 schematically illustratedin FIG. 98.

The DC current through the chamber is determined by two resistances: theinterface resistance R_(i) between the electrodes 860 and 870 and thebulk of the solution, and the solution resistance R_(s) which is derivedfrom the bulk solution resistivity and conduction path geometry. Forsolutions with ionic strengths relevant to the conditions in LOCdevices, the chamber resistance is dominated by interfacial resistancesat the electrodes 860 and 870, and R_(s) can be neglected.

The effect of the interfacial resistance is estimated by scalingmeasurements of macroscopic current flow through similar solutions forthe electrode geometries in the LOC devices.

Macroscopic measurements of current density through a similar solution,at platinum electrodes, were taken. Consistent with the worst-case (highcurrent) approach being taken, overall ionic strength and ECL reactantconcentrations in the test solution were higher than those used in theLOC devices. The anode area was smaller than the cathode area, and wassurrounded by a cathode with comparable area in a ring geometry. For ananode consisting of a circle 2 mm in diameter, the current measured was1.1 mA, giving a current density of 350 A/m².

In the heating model, the electrode area is for the square ring geometryschematically illustrated in FIG. 98. The anode is a ring with width 1μm and thickness 1 μm. The surface area is 196 square microns, andtherefore the calculated current I=69 nA.

The heating (power=V²/R) was modelled for the worst case in which allthe heat goes into raising the temperature of the water in the chamber.This leads to heating of chamber contents at 5.8° C./s, at a voltagedifference of 2.2 V, if no allowance for heat removal by the bulk of theLOC device is made.

Heating of the chambers by ˜20° C. can cause denaturation of mosthybridization probes. For highly specific probes intended for mutationdetection, it is preferable to further restrict heating to 4° C. orless. With this level of temperature stability, single basemismatch-sensitive hybridization, using appropriately designedsequences, becomes feasible. This allows the detection of mutations andallelic differences at the level of single nucleotide polymorphisms.Hence the DC current is applied to the electrodes 860 and 870 for 0.69s, to limit the heating to 4° C.

A current of ˜69 nA passing through the chamber is far more than can beaccommodated as Faradaic current by the ECL species at micromolarconcentrations. Therefore, low-duty-cycle pulsing of the electrodes 860and 870 to further reduce heating (to 1° C. or less) while maintainingsufficient ECL emission 862, does not introduce complications associatedwith reagent depletion. In other embodiments, the current is reduced to0.1 nA which removes the need for pulsed activation of the electrodes.Even at currents as low as 0.1 nA, the ECL emission 862 isluminophore-limited.

Chamber and Electrode Geometry Maximizing Optical Coupling Between ECLLuminescence and Photosensor

The immediate chemical precursors of ECL luminescence are generatedwithin nanometres of the working electrode. Referring again to FIG. 97,light emission (the excited species 868) generally occurs within micronsor less of that location. Hence the volume immediately adjacent to theworking electrode (anode 860) is visible to the corresponding photodiode184 of the photosensor 44. Accordingly, the electrodes 860 and 870 aredirectly adjacent the active surface area 185 of the correspondingphotodiode 184 in the photosensor 44. Furthermore, the anode 860 isshaped to increase the length of its lateral periphery ‘seen’ by thephotodiode 184. This aims to maximize the volume of excited species 868that can be detected by the underlying photodiode 184.

FIG. 96 schematically illustrates three embodiments of the anode 860. Acomb structure anode 878 has the advantage that the parallel fingers 880can be interdigitated with the fingers of a cathode 870. Theinterdigitated configuration is shown in FIG. 103, and in a partial viewof a LOC layout in FIGS. 120 and 124. The interdigitated configurationprovides a uniform dielectric gap 876 (see FIG. 97) that is relativelynarrow (1 to 2 microns) and the interdigitated comb structure isrelatively simple for the lithographic fabrication process. As discussedabove, a relatively narrow dielectric gap 876 between the electrodes 860and 870 obviates the need for a coreactant in some solutions 872, as theexcited species 868 will diffuse between anode and cathode. The removalof the requirement for a coreactant removes the potential chemicalimpact of the coreactant on the various assay chemistries and provides awider range of possible assay options.

Referring again to FIG. 96, some embodiments of the anode 860 have aserpentine configuration 882. To achieve high periphery length whilemaintaining tolerance against fabrication errors, it is convenient toform wide, rectangular meanders 884.

The anode may have a more complex configuration 886 if necessary ordesirable. For example, it may have a crenulated section 888, a branchedstructure 890, or a combination of the two. Partial views of LOC designsincorporating a branched structure 890 are shown in Figures 138 and 139.The more complicated configurations such as 886 provide a long length oflateral periphery, and are best suited to solution chemistries where acoreactant is employed since patterning a closely-spaced opposingcathode is more difficult.

Electrode Thickness

Generally, ECL cells involve a planar working electrode which is viewedexternally. Also, traditional microfabrication techniques for metallayers tend to lead to planar structures with metal thicknesses ofapproximately 1 micron. As has been indicated earlier, and shownschematically in FIGS. 96, 99 and 100, increasing the length of lateralperiphery enhances the coupling between the ECL emission and thephotodiode 184.

A second strategy to further increase the efficiency of collection ofemitted light 862 (see FIG. 130) by the photodiode 184 is to increasethe thickness of the anode 860. This is shown schematically in FIG. 97.The part of the participating volume 892 adjacent to the walls of theworking electrode is the region most efficiently coupled to thephotodiode 184. Therefore, for a given width of working electrode 860,the overall collection efficiency of the emitted light 862 can beimproved by increasing the thickness of the electrodes. Further, sincehigh current carrying capacity is not required, the width of the workingelectrode 860 is reduced as far as is practical. The thickness of theelectrodes 860 and 870 can not increase without restrictions. Notingthat the feature and separation sizes of the electrodes are likely to beof the order of 1 micron, and that liquid filling makes gaps which arewider than they are deep unfavourable, the optimum practical thicknessfor the electrodes is 0.25 micron to 2 microns.

Electrode Spacing

The spacing between the electrodes 860 and 870 is important for thequality of signals in LOC devices, particularly in embodiments where theelectrodes are interdigitated. In embodiments where the anode 860 is abranched structure such as shown in FIG. 96 and FIG. 100, the spacingbetween adjacent elements can also be important. ECL emissionefficiency, and the collection efficiency of the emitted light, shouldboth be maximised.

Generation of ECL emission tends to favour electrode spacings on theorder of one micron or less. Small spacings are particularly attractivewhen performing ECL in the absence of a coreactant. The fact that thespacing can be comparable to the wavelength of the emitted light 862 isof limited importance. Therefore, in many embodiments where the emittedlight 862 (see FIG. 130) is measured at a location which does notrequire that the light have passed between the electrodes 860 and 870,making the electrode spacing as small as practical is often the goal. Inembodiments where the emitted light 862 must pass between the electrodes860 and 870, however, it becomes necessary to move beyond consideringjust the ECL emission process, and consider the wave properties oflight.

The wavelength of the emitted light 862 from ECL of Ru(bpy)₃ ²⁺ isaround 620 nm, and therefore 460 nm (0.46 microns) in water. Inembodiments where the photodiode 184 and the ECL excited species 868 areon different sides of the electrode structure, and the electrodestructure is metallic, the emitted light 862 must pass through a gapbetween elements of the metallic structures. If this gap is comparableto the wavelength of the light, diffraction generally reduces theintensity of propagating light which reaches the photodiode 184. Incases where the emitted light 862 is incident on the gap at largeangles, however, evanescent mode coupling can be harnessed to improvethe strength of collected signals. Two measures are taken in the LOCdevices to enhance the efficiency of coupling between the photodiode 184and the emitted light 862.

First, the separation between metallic elements is not reduced belowapproximately the wavelength of the emitted light in water, i.e.approximately 0.4 microns. When combined with other observationsregarding small separations between interdigitated electrodes, thisindicates an optimal range for the electrode spacing of 0.4 to 2microns.

Second, the distance from the gap between elements to the photodiode 184is minimised. In the LOC device embodiments described here, thisindicates that the total thickness of layers between the electrodes 860and 870 and the photodiode 184 be one micron or less. In embodimentswhere multiple layers are present between the electrodes and thephotodiode, arranging their thicknesses to be quarter-wave orthree-quarter wave layers has the further benefit of suppressingreflection of the emitted light 862.

Electrode Models

FIG. 97 is a schematic partial cross-section of the electrodes 860 and870 in the hybridization chamber. The volume around the lateralperiphery of the anode 860 occupied by the excited species 868, issometimes referred to as the participating volume 892. The occludedregion 894 above the anode 860 is ignored because its optical couplingto the photodiode 184 is negligible.

A technique for determining whether a particular electrode configurationprovides a foundation for the level of ECL emission 862 for theunderlying photodiode 184 is set out below with reference to FIGS. 98,99 and 100.

FIG. 98 is a ring geometry in which the anode 860 is around the edge ofphotodiode 184. In FIG. 99, the anode 860 is positioned within theperiphery of the photodiode 184. FIG. 100 shows a more complexconfiguration in which the anode 860 has a series of parallel fingers880 to increase the length of its lateral edges.

For all of the above configurations, the model calculations are asfollows. For a participating volume 892 of solution V_(ECL), the totaleffective number of emitters N_(em) is:

N _(em) =N _(lum)·τ_(p)/τ_(ECL) =V _(ECL) C _(L) N _(A)·τ_(p)/τ_(ECL)  (6)

where the participating number of luminophoresM_(lum)=V_(ECL)C_(L)N_(A), τ_(ECL) is the lifetime of the ECL process,C_(L) is the luminophore concentration, τ_(p) is the pulse duration, andN_(A) is Avogadro' s number.

The number of isotropically emitted photons N_(phot) is:

N_(phot)=φ_(ECL)N_(em)   (7)

where φ_(ECL) is the ECL efficiency, defined as the average number ofphotons emitted by the ECL reaction of a single luminophore.

The signal count of electrons, S, from the photodiode is then

S=N_(phot)·φ_(o)φ_(q),   (8)

where φ_(o) is the optical coupling efficiency (the number of photonsabsorbed by the photodiode 184) and φ_(q) is the photodiode quantumefficiency. The signal is therefore:

$\begin{matrix}{S = {V_{ECL}C_{L}N_{A}\frac{\tau_{p}}{\tau_{ECL}}\varphi_{ECL}\varphi_{o}\varphi_{q}}} & (9)\end{matrix}$

For FIGS. 98 and 99 electrode configurations, φ_(o) is:

φhd o=(25% photons which are directed towards the photodiode 184)×(10%of photons which are not reflected)

i.e., φ_(o)=2.5% for configurations shown in FIGS. 98 and 99

For the electrode configuration of FIG. 100, 50% of photons are emittedin a direction pointing towards the photodiode 184, but the absorptionefficiency as a function of angle is unchanged, so

φ_(o)=(50% photons which are directed towards the photodiode)×(10% ofphotons which are not reflected)

i.e., φ_(o)=5% for the configuration of FIG. 100.

The participating volume 892 depends on the electrode configuration, anddetails are presented in the corresponding sections.

The input parameters for the calculations are listed in the following:

TABLE 5 Input Parameters Parameter Value Comment Luminophore concen-2.89 μM Probe concentration tration C_(L) calculated previously ECLrecycling period 1 ms Combined lifetimes of (lifetime) τ_(ECL) reactionsteps for luminophore. Boundary layer 0.5 μm Effective volume (includingdepth D diffusion and electro- phoresis) of solution participating inECL Duration of current 0.69 s Chosen to limit ohmic application τ_(p)heating to 4° C. (as described previously) Chamber X dimension 28 μmChamber Y dimension 28 μm Chamber height Z 8 μm Photodiode X dimension16 μm Photodiode Y dimension 16 μm Electrode thickness (i.e., 1 μmexposed edge height) Electrode layer minimum 1 μm Process critical widthand gap dimension Electrode interfacial 350 A/m² For ohmic heatingcurrent density Solution volume 0.5 Ω · m For ohmic heating resistivityVoltage difference 2.2 V applied (working − counter electrode)

Ring Geometry Around Periphery of Photodiode

Referring to FIG. 98, the anode 860 is a ring around the edge of thephotodiode 184. In this configuration, the participating volume 892 is:

V _(ECL)=4×[(layer beside the electrode wall)+(quarter-cylinder abovethe electrode wall)]

Calculation results:

-   Photons generated from a 0.5 μm boundary layer: 3.1×10⁵-   Electron counts in photodiode: 2.3×10³

This signal is readily detectable by the underlying photodiode 184 ofthe LOC device photosensor 44.

Additional Fingers to Increase Edge Length

Referring to FIG. 100, parallel fingers 880 are added across the anode860. Only horizontal edges shown in figure contribute to theparticipating volume 892, to avoid double-counting the perpendicularedges. The participating volume 892 is then:

V _(ECL)=(8×2)×[(layer beside the electrode wall)+(quarter-cylinderabove the electrode wall)]

Calculation results for FIG. 100 configuration:

-   Photons generated from a 0.5 μm boundary layer: 1.1×10⁶-   Electron counts in photodiode 184: 8.0×10³

This signal is easily detectable in the photodiode 184.

Complete Overlay

This configuration shown in FIG. 101 and FIG. 102 is included as alimiting case of maximum surface area coupling. In practice, 90% orbetter coupling between the electrode surface area and the activesurface area 185 of the photodiode 184 achieves a nearly optimal result,and even coupling of 50% of the photodiode active surface area 185 tothe electrode surface area provides most of the benefit of the completeoverlay configuration. Complete overlay can be achieved in twoembodiments: first, as indicated schematically in FIG. 101, by employinga transparent anode 860, in a plane parallel with that of the photodiode184 and with an area matched to that of the photodiode, and arrangingthe anode in immediate proximity to the photodiode 184, such thatemitted light 862 passes through the anode and onto the photodiode. In asecond embodiment shown schematically in FIG. 102, the anode 860 isagain parallel to and registered with the photodiode area, but thesolution 872 fills a void between the anode 860 and the photodiode 184.For signal modelling of a complete overlay configuration, the anode isassumed to be a complete layer above the photodiode 184, with half ofthe photons directed toward the photodiode 184 (absorption efficiencystill 10%).

-   Photons generated from a 0.5 μm boundary layer: 7.7×10⁵-   Electron counts in photodiode: 1.2×10⁴

It is possible to improve the signal and assay beyond the above modelsby using surfactants and probe immobilization at the anode.

Maximum Spacing Between ECL Probes and Photodiode

The on-chip detection of hybridization avoids the needs for detectionvia confocal microscopy (see Background of the Invention). Thisdeparture from traditional detection techniques is a significant factorin the time and cost savings associated with this system. Traditionaldetection requires imaging optics which necessarily uses lenses orcurved mirrors. By adopting non-imaging optics, the diagnostic systemavoids the need for a complex and bulky optical train. Positioning thephotodiode very close to the probes has the advantage of extremely highcollection efficiency: when the thickness of the material between theprobes and the photodiode is on the order of 1 micron, the angle ofcollection of emission light is up to 174°. This angle is calculated byconsidering light emitted from a probe at the centroid of the face ofthe hybridization chamber closest to the photodiode, which has a planaractive surface parallel to that chamber face. The cone of emissionangles within which light is able to be absorbed by the photodiode isdefined as having the emitting probe at its vertex and the corner of thesensor on the perimeter of its planar face. For a 16 micron×16 micronsensor, the vertex angle of this cone is 170°; in the limiting casewhere the photodiode is expanded so that its area matches that of the 28micron×26.5 micron hybridization chamber, the vertex angle is 174°. Aseparation between the chamber face and the photodiode active surface of1 micron or less is readily achievable.

Employing a non-imaging optics scheme does require the photodiode 184 tobe very close to the hybridization chamber in order to collectsufficient photons of fluorescence emission. The maximum spacing betweenthe photodiode and probes is determined as follows.

Utilizing a ruthenium chelate luminophore and the electrodeconfiguration of FIG. 100, we calculated 27,000 photons being absorbedby our 16 micron×16 micron sensor from the respective hybridizationchamber, to generate 8000 electrons assuming a sensor quantum efficiencyof 30%. In performing this calculation we assumed that thelight-collecting region of our hybridization chamber has a base areawhich is the same as our sensor area, one quarter of the total number ofthe hybridization photons is angled so as to reach the sensor, and aconservative 10% estimate for the proportion of photons which do notscatter away from the sensor-dielectric interface. That is, the lightgathering efficiency of the optical system is φ₀=0.025.

More accurately we can write φ₀=[(base area of the light-collectingregion of the hybridization chamber)/(photodetector area)][Ω/4π][10%absorbed], where Ω=solid angle subtended by the photodetector at arepresentative point on the base of the hybridization chamber. For aright square pyramid geometry:

Ω=4 arcsin(a ²/(4d ₀ ² +a ²)), where d₀=distance between the chamber andthe photodiode, a is the photodiode dimension.

Each hybridization chamber releases 1.1×10⁶ photons. The selectedphotodetector has a detection threshold of 17 photons, and for values ofd₀ greater than ten times the sensor size (i.e., essentially normalincidence) the proportion of photons not reflected at the sensor surfacecan be increased from 10% to 90%. Therefore, the minimum opticalefficiency required is:

φ₀=17/(1.1×10⁶×0.9)=1.72×10⁻⁵

The base area of the light-emitting region of the hybridization chamber180 is 29 micron×19.75 micron.

Solving for d₀, we will get the maximum limiting distance between thebottom of our hybridization chamber and our photodetector to be d₀=1600microns. In this limit, the collection cone angle as defined above isonly 0.8°. It should be noted this analysis ignores the negligibleeffect of refraction.

LOC Variants

The LOC device 301 described and illustrated above in full is just oneof many possible LOC device designs. Variations of the LOC device thatuse different combinations of the various functional sections describedabove will now be described and/or shown as schematic flow-charts, fromsample inlet to detection, to illustrate some of the combinationspossible. The flow-charts have been divided, where appropriate, intosample input and preparation stage 288, extraction stage 290, incubationstage 291, amplification stage 292, pre-hybridization stage 293 anddetection stage 294. For all the LOC variants that are briefly describedor shown only in schematic form, the accompanying full layouts are notshown for reasons of clarity and succinctness. Also in the interests ofclarity, smaller functional units such as liquid sensors and temperaturesensors are not shown but it will be appreciated that these have beenincorporated into the appropriate locations in each of the following LOCdevice designs.

LOC Device with ECL Detection

FIGS. 111 to 127 show a LOC variant 729 with electrochemiluminescence(ECL) detection. This LOC device prepares 288, extracts 290, incubates291, amplifies 292 and detects 294 both human and pathogen nucleicacids, as well as human and pathogen protein detection. ECL is used inthe hybridization chamber arrays and proteomic assay chamber arrays fortarget detection.

As best shown in FIG. 117, a biological sample (for example, wholeblood) is added to the sample inlet 68. The sample flows through the capchannel 94 to the anticoagulant surface tension valve 118. The cap 46 isfabricated with an interface layer 594 positioned between the capchannel layer 80 and the MST channel layer 100 of the CMOS+MST device 48(see FIG. 112). The interface layer 594 allows a more complex fluidicinterconnection between the reagent reservoirs and the MST layer 87without increasing the size of the silicon substrate 84.

FIG. 113 shows the MST layer 87 visible on the top surface of theCMOS+MST device 48. FIG. 114 shows the cap channel layer 80 on theunderside of the cap 46. FIG. 115 superimposes the reservoirs, the capchannels 94 and the interface channels to illustrate the moresophisticated plumbing achieved with a cap 46 incorporating an interfacelayer 594.

As best shown in FIG. 117, the interface layer 594 requires theanticoagulant surface tension valve 118 to have two interface channels596 and 598. A reservoir-side interface channel 596 connects thereservoir outlet with the downtakes 92 and a sample-side interfacechannel 598 connects the uptakes 96 with the cap channel 94.

Anticoagulant from the reservoir 54 flows through the MST channels 90via the reservoir-side interface channel 596 to pin a meniscus at theuptakes 96. The sample flow along the cap channel 94 dips into thesample-side interface channel 598 to remove the meniscus so that theanticoagulant combines with the blood sample as it continues onto theleukocyte dialysis section 328.

The leukocyte dialysis section 328 incorporates a bypass channel 600 forfilling the flow channel structures without trapped air bubbles (seeFIGS. 117 and 126). The blood sample flows through cap channel 94 to theupstream end of the large constituents interface channel 730. The largeconstituents interface channel 730 is in fluid communication with thedialysis MST channels 204 via apertures in the form of 7.5 microndiameter holes 165(see FIG. 126).

Referring to FIG. 126, each of the dialysis MST channels 204 lead fromthe 7.5 micron diameter holes 165 to respective dialysis uptakes 168.The dialysis uptake holes 168 are open to the small constituentsinterface channel 732. However the uptakes are configured to pin ameniscus rather than allow capillary driven flow to continue. The uptakebelonging to the bypass channel 600 has a capillary initiation feature202 configured to initiate capillary driven flow into the smallconstituents interface channel 732. This ensures the flow begins at theupstream end of the small constituents interface channel 732 andsequentially unpins the menisci at the dialysis uptakes 168 as the flowprogresses downstream.

FIG. 121 shows the downstream end of the leukocyte dialysis section 328.The large constituents interface channel 730 feeds into the largeconstituents cap channel 736 and the small constituents interfacechannel 732 feeds the small constituents cap channel 734. As best shownin FIG. 115, the large constituents cap channel 736 feeds the leukocytes(and any other large constituents) into the chemical lysis section 130.1via the lysis surface tension valve 128.1 where lysis reagent fromreservoir 56.1 is added. The chemical lysis section 130.1 has a 3 micronfilter downtake 738 at the outlet (see FIG. 117). The filter downtakeensures that no large constituents reach the lysis chamber exitboiling-initiated valve 206. After sufficient time, theboiling-initiated valve 206 opens the chemical lysis section 130.1outlet and the sample flow is split into two streams. As best shown inFIG. 117, one stream flows to the surface tension valve 132.1 for thefirst restriction enzyme, ligase and linker reservoir 58.1 and the otherstream is drawn along a lysed leukocyte bypass channel 742 directly tothe proteomic assay chamber array 124.1 in the hybridization anddetection section 294. Here the sample fills the proteomic assay chamberarray 124.1 (see FIG. 119) containing probes for hybridization withtarget human proteins. Probe-target hybrids are detected with aphotosensor 44 (see FIG. 111). The other stream flows into the leukocyteincubation section 114.1 together with restriction enzymes, ligase andlinker primers from reservoir 58.1.

Referring to FIG. 118, after restriction enzyme digestion and linkerligation, the incubator outlet valve 207 (also a boiling-initiatedvalve) opens and flow continues into the leukocyte DNA amplificationsection 112.1. The amplification mix and polymerase in reservoirs 60.1and 62.1 are added via surface tension valves 138.1 and 140.1respectively. Referring to FIG. 119, after thermal cycling, theboiling-initiated valve 108 opens for the amplicon to enter thehybridization chamber array 110.1 containing probes for human DNAtargets. Probe-target hybrids are detected with the photosensor 44.

The erythrocytes and pathogens from the leukocyte dialysis section 328are fed to the pathogen dialysis section 70 via the cap channel 734 (seeFIGS. 117 and 127). This operates in the same manner as the leukocytedialysis section 328 with the exception that the filter downtakes have 3micron holes 164 instead of the 7.5 micron holes 165 used for leukocytedialysis. The erythrocytes remain in the large constituents interfacechannel 730 while the pathogens diffuse to the small constituentsinterface channel 732.

FIG. 122 shows the downstream end of the pathogen dialysis section 70.The erythrocytes flow into the large constituents cap channel 736 andthe pathogens fill the small constituents cap channel 734. It will beappreciated that ‘large constituents’ and ‘small constituents’ are usedin a relative sense as the large constituents output of the pathogendialysis section is part of the small constituents output of theleukocyte dialysis section. The constituents in the large constituentscap 736 or interface channels are simply larger than the constituents inthe small constituents cap 734 or interface channels within thatparticular dialysis section. As best shown in FIGS. 115 and 116, theerythrocytes in the large constituents cap channel 736 are directed tothe surface tension valve 128.3 for the lysis reagent reservoir 56.3.The lysis reagent combines with the erythrocytes as the sample fluidfills the chemical lysis section 130.3. Boiling-initiated valve 206 atthe outlet of the third chemical lysis section 130.3 retains thepathogens until lysis is complete. When the boiling-initiated valve 206opens, the erythrocyte DNA flows directly into the proteomic assaychamber array 124.3 for protein analysis and detection by thephotosensor 44 (see FIG. 119).

The pathogens in the small constituents cap channel 734 are directed tothe surface tension valve 128.2 of the second lysis reagent reservoir56.2. The lysis reagent combines with the pathogens as the sample fluidfills the second chemical lysis section 130.2. After sufficient time,the boiling-initiated valve 206 opens the chemical lysis section 130.2outlet and the sample flow is split into two streams. As best shown inFIGS. 116 and 118, one stream flows to the surface tension valve 132.2for the second restriction enzyme, ligase and linker reservoir 58.2 andthe other stream is drawn along a bypass channel 744 directly to thehybridization and detection section 294. Here the sample fills theproteomic assay chamber array 124.2 (see FIG. 119) containing probes forhybridization with target pathogen proteins or other biomolecules.Probe-target hybrids are detected with the photosensor 44 (see FIG.111).

The other stream flows into the pathogen incubation section 114.2together with restriction enzymes, ligase and linker primers fromreservoir 58.2. After restriction digestion and linker ligation, theincubator exit valve 207 (also a boiling-initiated valve) opens and flowcontinues into the pathogenic DNA amplification section 112.2 (see FIG.118). As the chamber fills, the amplification mix and polymerase inreservoirs 60.2 and 62.2 are added via surface tension valves 138.2 and140.2 respectively. After thermal cycling, the boiling-initiated valve108 opens for the amplicon to flow into the second hybridization chamberarray 110.2 containing probes for pathogenic DNA targets. Probe-targethybrids are detected with the photosensor 44 (see FIG. 119).

Referring to FIG. 120, the hybridization chamber arrays 110.1 and 110.2and proteomic assay chamber arrays 124.1 to 124.3 have heater elements182 made from strips of titanium nitride. There are end-point liquidsensors 178 that detect when the flow has reached the end of thehybridization chamber array or proteomic assay chamber array and theheaters 182 are then activated after a time delay. The flow rate sensor740 (see FIG. 125) is included in the pathogen incubation section 114.2to determine the time delay.

FIGS. 123 and 124 show the calibration chambers 382. They are used tocalibrate the photodiodes 184 to adjust for system noise and backgroundlevels. The photodiode's response and electrical noise characteristicscan vary with location and due to thermal variations. The output signalfrom calibration chambers 382, which do not contain any probes, closelyapproximates the noise and background in the output signal from all thechambers. Subtracting the calibration signal from the output signalsgenerated by the other hybridization chambers substantially removes thenoise and leaves the signal generated by the electrochemiluminescence(if any). Also, positive and negative control ECL probes 786 and 787 canbe placed in some of the hybridization chambers 180 for assay qualitycontrol.

Referring to FIG. 116, a humidifier 196, composed of the water reservoir188 and evaporators 190, is located in the top left of the device. Theposition of the humidity sensor 232 is adjacent to the hybridizationchamber array 110 where humidity measurement is most important to slowevaporation from the solution containing the exposed probes.

By combining the leukocyte and pathogen output dialysis sections, threeoutput streams are produced (leukocytes, erythrocytes, and pathogens andother biomolecules) which are processed separately to enable highersensitivity and parallel analysis. The output from each stream is lysedand separately directed to the proteomic assay chamber arrays forprotein detection. The lysed leukocytes and pathogens are alsoseparately directed to the incubation 114 and amplification 112 sectionsfor amplification, followed by hybridization for nucleic acid detection.

LOC Device with Thermal Insulation Trench

As best depicted in FIG. 128, a trench 896 is etched into the back ofthe silicon substrate 84. The purpose of the trench is to thermallyinsulate the amplification section 112 from the hybridization chamberarray 110. The hybridization array contains detection probes that candegrade at high temperatures. The trench, when filled with air, has athermal conductivity of the order of 6000 times less than that of thesilicon substrate, thereby significantly reducing the heat flux intoadjacent parts of the LOC device.

This provides two main advantages: an increase in the heating efficiencyin the amplification section 112; and a reduction in the undesirabletemperature rise of the adjacent hybridization section 110. Improvedheating efficiency means less power is required to heat theamplification section 112 and the temperature reaches its desiredend-point temperature faster and with better spatial uniformity withinthe amplification section. A reduction in the temperature rise in thehybridization section 110 allows for a wider range of probe chemistriesand superior signal quality.

The trench can be placed around any region on the LOC device tothermally insulate the components in that region. The width and depth ofthe trench 896 are variable to suit the specific application.

Conclusion

The devices, systems and methods described here facilitate moleculardiagnostic tests at low cost with high speed and at the point-of-care.

The system and its components described above are purely illustrativeand the skilled worker in this field will readily recognize manyvariations and modifications which do not depart from the spirit andscope of the broad inventive concept.

1. A lab-on-a-chip (LOC) device for amplifying and detecting targetnucleic acid sequences, the LOC device comprising:electrochemiluminescent (ECL), resonant energy transfer, stem-and-loopprobes for hybridization with the target nucleic acid sequences, each ofthe probes having a loop portion containing a sequence complementary tothe target nucleic acid sequence, an ECL luminophore for emittingphotons when in an excited state, a functional moiety for quenchingphoton emission from the ECL luminophore by resonant energy transfer,and a covalently attached primer for extension along a complementarysequence denatured from the target nucleic acid sequence to replicatethe target nucleic acid sequence; heaters for thermally cycling thetarget nucleic acid sequences through a polymerase chain reaction (PCR),in which the covalently attached primers anneal to oligonucleotidescontaining the target nucleic acid sequences; and, electrodes forreceiving an electrical pulse to excite the ECL luminophores; whereinduring use, replicating the target nucleic acid sequence causes the loopportion to open such the complementary nucleic acid sequence thereinhybridizes to the target nucleic acid sequence and the ECL luminophoreis moved away from the functional moiety.
 2. The LOC device according toclaim 1 further comprising: a photosensor for detecting light emitted bythe ECL luminophores.
 3. The LOC device according to claim 2 furthercomprising: a supporting substrate; CMOS circuitry for activating theheaters and providing the electrodes with an electrical pulse;hybridization chambers containing the probes for hybridization with thetargets, at least one of the heaters and a pair of the electrodes; and,a flow-path for fluid containing the targets; wherein, the CMOScircuitry is between the hybridization chambers and the supportingsubstrate, and the flow-path draws the fluid to each of thehybridization chambers by capillary action.
 4. The LOC device accordingto claim 3 further comprising a lysis section wherein the fluid is abiological sample containing cells and the lysis section disrupts thecellular membranes to release any genetic material therein.
 5. The LOCdevice according to claim 4 wherein the hybridization chambers each havea wall section that is optically transparent to the light emitted by theprobes.
 6. The LOC device according to claim 5 wherein the CMOScircuitry incorporates the photosensor wherein the wall section ispositioned between the probes and the photosensor.
 7. The LOC deviceaccording to claim 5 wherein the wall section is a layer incorporatingsilicon dioxide.
 8. The LOC device according to claim 2 wherein thecovalently attached primer is attached to the functional moiety forquenching photon emission from the ECL luminophore and the loop portionis between the ECL luminophore and the functional moiety.
 9. The LOCdevice according to claim 8 wherein the CMOS circuitry is configured toprovide an electrical pulse to the electrodes.
 10. The LOC deviceaccording to claim 9 wherein the electrical pulse has a duration lessthan 0.69 seconds.
 11. The LOC device according to claim 7 wherein theelectrical pulse has a current of 0.1 nanoamperes to 69.0 nanoamperes.12. The LOC device according to claim 9 wherein the electrodes have ananode and a cathode each having fingers configured such that the fingersof the anode are interdigitated with the fingers of the cathode.
 13. TheLOC device according to claim 12 wherein the anode and the cathode areseparated by a dielectric gap between 0.4 microns and 2 microns wide.14. The LOC device according to claim 4 wherein the transparent wallsection is less than 1600 microns thick.
 15. The LOC device according toclaim 2 wherein the photosensor is an array of photodiodes positioned inregistration with the hybridization chambers such that each of thehybridization chambers corresponds to one of the photodiodesrespectively.
 16. The LOC device according to claim 15 wherein thephotodiodes each have a planar active surface area such that the planaractive surface areas collectively provide the collection surface, eachof the active surface areas being coplanar, and the electrodes are alayer of conductive material patterned to form the separate anodes andcathodes, the layer extending in a plane parallel to that of the activesurface areas of the photodiodes.
 17. The LOC device according to claim15 wherein one of the electrodes in each of the electrode pairs is aworking electrode which causes oxidation or reduction of the luminophoreto generate an excited species that emits a photon, the workingelectrode being positioned such that the probes are between thephotodiode and the working electrode.
 18. The LOC device according toclaim 1 wherein the luminophore is a metalorganic complex.
 19. The LOCdevice according to claim 18 wherein the metalorganic complex is aruthenium organic complex molecule.
 20. The LOC device according toclaim 4 further comprising a dialysis section for diverting the cellssmaller than a predetermined size threshold into a separate stream.